Ben Bolstad
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:06 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2025-12-12 01:38:37 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 01:39:48 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 71.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.74.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... WARNING
Found the following significant warnings:
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.574 0.204 0.756
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 480714 25.7 1056242 56.5 NA 634451 33.9
Vcells 890616 6.8 8388608 64.0 65536 2108808 16.1
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri Dec 12 01:39:10 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri Dec 12 01:39:10 2025"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x600001150000>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri Dec 12 01:39:16 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri Dec 12 01:39:19 2025"
>
> ColMode(tmp2)
<pointer: 0x600001150000>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.54313459 -0.5384308 -0.62715076 -0.5718972
[2,] -1.10540426 -0.2869039 -0.17955279 -0.2723187
[3,] -0.36717491 -0.6365842 0.50102130 -0.5386739
[4,] -0.07230638 0.7945292 0.05541926 -0.7094786
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.54313459 0.5384308 0.62715076 0.5718972
[2,] 1.10540426 0.2869039 0.17955279 0.2723187
[3,] 0.36717491 0.6365842 0.50102130 0.5386739
[4,] 0.07230638 0.7945292 0.05541926 0.7094786
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9771306 0.7337785 0.7919285 0.7562389
[2,] 1.0513821 0.5356342 0.4237367 0.5218417
[3,] 0.6059496 0.7978623 0.7078286 0.7339441
[4,] 0.2688985 0.8913637 0.2354130 0.8423055
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.31444 32.87622 33.54644 33.13429
[2,] 36.61922 30.64325 29.41692 30.49074
[3,] 31.42667 33.61521 32.57931 32.87811
[4,] 27.76129 34.70817 27.40955 34.13253
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x60000117c300>
> exp(tmp5)
<pointer: 0x60000117c300>
> log(tmp5,2)
<pointer: 0x60000117c300>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 466.8811
> Min(tmp5)
[1] 53.70916
> mean(tmp5)
[1] 72.96512
> Sum(tmp5)
[1] 14593.02
> Var(tmp5)
[1] 859.8669
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.21131 70.57667 69.53158 68.08061 69.58621 70.45516 73.25521 72.26370
[9] 70.25969 75.43108
> rowSums(tmp5)
[1] 1804.226 1411.533 1390.632 1361.612 1391.724 1409.103 1465.104 1445.274
[9] 1405.194 1508.622
> rowVars(tmp5)
[1] 7906.91364 51.63604 58.15983 85.72467 84.37827 64.11930
[7] 76.45245 84.62373 98.68768 105.30280
> rowSd(tmp5)
[1] 88.920828 7.185822 7.626259 9.258762 9.185764 8.007453 8.743709
[8] 9.199116 9.934168 10.261715
> rowMax(tmp5)
[1] 466.88112 85.91310 86.79763 86.61995 85.53251 89.60265 92.83441
[8] 84.47388 89.38214 90.35264
> rowMin(tmp5)
[1] 57.55651 60.04450 54.56885 56.24526 53.81978 59.54636 63.24996 57.61913
[9] 53.70916 58.96955
>
> colMeans(tmp5)
[1] 113.63404 72.97707 65.58329 71.43793 74.45170 72.93953 66.52942
[8] 70.92396 69.11527 70.85276 71.13619 70.35144 76.30302 73.27855
[15] 68.36039 72.83278 67.88065 73.75929 65.95636 70.99882
> colSums(tmp5)
[1] 1136.3404 729.7707 655.8329 714.3793 744.5170 729.3953 665.2942
[8] 709.2396 691.1527 708.5276 711.3619 703.5144 763.0302 732.7855
[15] 683.6039 728.3278 678.8065 737.5929 659.5636 709.9882
> colVars(tmp5)
[1] 15492.78771 64.65130 40.86982 16.41487 158.50991 38.23756
[7] 35.38821 75.71539 83.34895 34.29062 74.55877 58.14761
[13] 88.71212 58.51938 96.35086 98.49458 103.97264 117.97730
[19] 105.91623 58.66750
> colSd(tmp5)
[1] 124.470027 8.040603 6.392951 4.051526 12.590072 6.183652
[7] 5.948799 8.701459 9.129564 5.855819 8.634742 7.625458
[13] 9.418711 7.649796 9.815847 9.924444 10.196698 10.861735
[19] 10.291561 7.659471
> colMax(tmp5)
[1] 466.88112 87.93001 78.77212 76.43935 89.42076 84.85980 73.66074
[8] 85.53251 90.35264 79.38450 81.53711 82.36814 87.91225 85.70105
[15] 89.38214 92.83441 80.59191 87.55536 89.60265 82.06178
> colMin(tmp5)
[1] 57.78149 62.05014 57.04938 63.46247 54.76101 63.65812 54.09239 59.81191
[9] 56.24526 63.24996 58.90901 60.11638 58.16902 63.69592 56.77448 60.29286
[17] 53.81978 58.96955 53.70916 60.78161
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 90.21131 70.57667 69.53158 68.08061 69.58621 70.45516 NA 72.26370
[9] 70.25969 75.43108
> rowSums(tmp5)
[1] 1804.226 1411.533 1390.632 1361.612 1391.724 1409.103 NA 1445.274
[9] 1405.194 1508.622
> rowVars(tmp5)
[1] 7906.91364 51.63604 58.15983 85.72467 84.37827 64.11930
[7] 80.68666 84.62373 98.68768 105.30280
> rowSd(tmp5)
[1] 88.920828 7.185822 7.626259 9.258762 9.185764 8.007453 8.982575
[8] 9.199116 9.934168 10.261715
> rowMax(tmp5)
[1] 466.88112 85.91310 86.79763 86.61995 85.53251 89.60265 NA
[8] 84.47388 89.38214 90.35264
> rowMin(tmp5)
[1] 57.55651 60.04450 54.56885 56.24526 53.81978 59.54636 NA 57.61913
[9] 53.70916 58.96955
>
> colMeans(tmp5)
[1] 113.63404 NA 65.58329 71.43793 74.45170 72.93953 66.52942
[8] 70.92396 69.11527 70.85276 71.13619 70.35144 76.30302 73.27855
[15] 68.36039 72.83278 67.88065 73.75929 65.95636 70.99882
> colSums(tmp5)
[1] 1136.3404 NA 655.8329 714.3793 744.5170 729.3953 665.2942
[8] 709.2396 691.1527 708.5276 711.3619 703.5144 763.0302 732.7855
[15] 683.6039 728.3278 678.8065 737.5929 659.5636 709.9882
> colVars(tmp5)
[1] 15492.78771 NA 40.86982 16.41487 158.50991 38.23756
[7] 35.38821 75.71539 83.34895 34.29062 74.55877 58.14761
[13] 88.71212 58.51938 96.35086 98.49458 103.97264 117.97730
[19] 105.91623 58.66750
> colSd(tmp5)
[1] 124.470027 NA 6.392951 4.051526 12.590072 6.183652
[7] 5.948799 8.701459 9.129564 5.855819 8.634742 7.625458
[13] 9.418711 7.649796 9.815847 9.924444 10.196698 10.861735
[19] 10.291561 7.659471
> colMax(tmp5)
[1] 466.88112 NA 78.77212 76.43935 89.42076 84.85980 73.66074
[8] 85.53251 90.35264 79.38450 81.53711 82.36814 87.91225 85.70105
[15] 89.38214 92.83441 80.59191 87.55536 89.60265 82.06178
> colMin(tmp5)
[1] 57.78149 NA 57.04938 63.46247 54.76101 63.65812 54.09239 59.81191
[9] 56.24526 63.24996 58.90901 60.11638 58.16902 63.69592 56.77448 60.29286
[17] 53.81978 58.96955 53.70916 60.78161
>
> Max(tmp5,na.rm=TRUE)
[1] 466.8811
> Min(tmp5,na.rm=TRUE)
[1] 53.70916
> mean(tmp5,na.rm=TRUE)
[1] 72.96605
> Sum(tmp5,na.rm=TRUE)
[1] 14520.24
> Var(tmp5,na.rm=TRUE)
[1] 864.2094
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.21131 70.57667 69.53158 68.08061 69.58621 70.45516 73.28017 72.26370
[9] 70.25969 75.43108
> rowSums(tmp5,na.rm=TRUE)
[1] 1804.226 1411.533 1390.632 1361.612 1391.724 1409.103 1392.323 1445.274
[9] 1405.194 1508.622
> rowVars(tmp5,na.rm=TRUE)
[1] 7906.91364 51.63604 58.15983 85.72467 84.37827 64.11930
[7] 80.68666 84.62373 98.68768 105.30280
> rowSd(tmp5,na.rm=TRUE)
[1] 88.920828 7.185822 7.626259 9.258762 9.185764 8.007453 8.982575
[8] 9.199116 9.934168 10.261715
> rowMax(tmp5,na.rm=TRUE)
[1] 466.88112 85.91310 86.79763 86.61995 85.53251 89.60265 92.83441
[8] 84.47388 89.38214 90.35264
> rowMin(tmp5,na.rm=TRUE)
[1] 57.55651 60.04450 54.56885 56.24526 53.81978 59.54636 63.24996 57.61913
[9] 53.70916 58.96955
>
> colMeans(tmp5,na.rm=TRUE)
[1] 113.63404 72.99886 65.58329 71.43793 74.45170 72.93953 66.52942
[8] 70.92396 69.11527 70.85276 71.13619 70.35144 76.30302 73.27855
[15] 68.36039 72.83278 67.88065 73.75929 65.95636 70.99882
> colSums(tmp5,na.rm=TRUE)
[1] 1136.3404 656.9897 655.8329 714.3793 744.5170 729.3953 665.2942
[8] 709.2396 691.1527 708.5276 711.3619 703.5144 763.0302 732.7855
[15] 683.6039 728.3278 678.8065 737.5929 659.5636 709.9882
> colVars(tmp5,na.rm=TRUE)
[1] 15492.78771 72.72737 40.86982 16.41487 158.50991 38.23756
[7] 35.38821 75.71539 83.34895 34.29062 74.55877 58.14761
[13] 88.71212 58.51938 96.35086 98.49458 103.97264 117.97730
[19] 105.91623 58.66750
> colSd(tmp5,na.rm=TRUE)
[1] 124.470027 8.528034 6.392951 4.051526 12.590072 6.183652
[7] 5.948799 8.701459 9.129564 5.855819 8.634742 7.625458
[13] 9.418711 7.649796 9.815847 9.924444 10.196698 10.861735
[19] 10.291561 7.659471
> colMax(tmp5,na.rm=TRUE)
[1] 466.88112 87.93001 78.77212 76.43935 89.42076 84.85980 73.66074
[8] 85.53251 90.35264 79.38450 81.53711 82.36814 87.91225 85.70105
[15] 89.38214 92.83441 80.59191 87.55536 89.60265 82.06178
> colMin(tmp5,na.rm=TRUE)
[1] 57.78149 62.05014 57.04938 63.46247 54.76101 63.65812 54.09239 59.81191
[9] 56.24526 63.24996 58.90901 60.11638 58.16902 63.69592 56.77448 60.29286
[17] 53.81978 58.96955 53.70916 60.78161
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.21131 70.57667 69.53158 68.08061 69.58621 70.45516 NaN 72.26370
[9] 70.25969 75.43108
> rowSums(tmp5,na.rm=TRUE)
[1] 1804.226 1411.533 1390.632 1361.612 1391.724 1409.103 0.000 1445.274
[9] 1405.194 1508.622
> rowVars(tmp5,na.rm=TRUE)
[1] 7906.91364 51.63604 58.15983 85.72467 84.37827 64.11930
[7] NA 84.62373 98.68768 105.30280
> rowSd(tmp5,na.rm=TRUE)
[1] 88.920828 7.185822 7.626259 9.258762 9.185764 8.007453 NA
[8] 9.199116 9.934168 10.261715
> rowMax(tmp5,na.rm=TRUE)
[1] 466.88112 85.91310 86.79763 86.61995 85.53251 89.60265 NA
[8] 84.47388 89.38214 90.35264
> rowMin(tmp5,na.rm=TRUE)
[1] 57.55651 60.04450 54.56885 56.24526 53.81978 59.54636 NA 57.61913
[9] 53.70916 58.96955
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.88059 NaN 64.99507 71.06152 75.37240 71.61505 66.79045
[8] 70.24001 68.87832 71.69752 70.85481 69.81056 77.44441 74.34329
[15] 68.71245 70.61038 68.30472 72.49013 65.78769 69.76961
> colSums(tmp5,na.rm=TRUE)
[1] 1051.9253 0.0000 584.9556 639.5537 678.3516 644.5355 601.1140
[8] 632.1601 619.9049 645.2776 637.6933 628.2950 696.9997 669.0896
[15] 618.4121 635.4934 614.7425 652.4111 592.0892 627.9265
> colVars(tmp5,na.rm=TRUE)
[1] 17310.80996 NA 42.08600 16.87284 168.78714 23.28213
[7] 39.04520 79.91721 93.13593 30.54881 82.98789 62.12486
[13] 85.14512 53.08058 107.00031 55.24178 114.94606 114.60331
[19] 118.83568 49.00247
> colSd(tmp5,na.rm=TRUE)
[1] 131.570551 NA 6.487373 4.107657 12.991811 4.825156
[7] 6.248616 8.939642 9.650696 5.527098 9.109769 7.881932
[13] 9.227411 7.285642 10.344095 7.432481 10.721290 10.705293
[19] 10.901178 7.000177
> colMax(tmp5,na.rm=TRUE)
[1] 466.88112 -Inf 78.77212 76.43935 89.42076 80.06832 73.66074
[8] 85.53251 90.35264 79.38450 81.53711 82.36814 87.91225 85.70105
[15] 89.38214 84.25110 80.59191 87.55536 89.60265 81.35614
> colMin(tmp5,na.rm=TRUE)
[1] 57.78149 Inf 57.04938 63.46247 54.76101 63.65812 54.09239 59.81191
[9] 56.24526 64.14666 58.90901 60.11638 58.16902 63.71760 56.77448 60.29286
[17] 53.81978 58.96955 53.70916 60.78161
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 295.4286 221.6697 164.4959 261.0815 255.8511 135.8989 193.9538 336.6189
[9] 128.8698 298.8430
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 295.4286 221.6697 164.4959 261.0815 255.8511 135.8989 193.9538 336.6189
[9] 128.8698 298.8430
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 0.000000e+00 -2.842171e-14 5.684342e-14 1.136868e-13 -5.684342e-14
[6] -5.684342e-14 0.000000e+00 2.842171e-14 -5.684342e-14 1.136868e-13
[11] -5.684342e-14 -1.705303e-13 7.105427e-14 1.705303e-13 1.989520e-13
[16] 0.000000e+00 -1.136868e-13 -2.842171e-14 0.000000e+00 -8.526513e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
9 7
7 1
7 11
9 4
1 14
8 1
4 7
8 10
8 16
3 16
5 14
8 6
3 19
10 10
4 9
1 16
2 2
2 14
2 3
5 10
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.170585
> Min(tmp)
[1] -3.096631
> mean(tmp)
[1] -0.06412957
> Sum(tmp)
[1] -6.412957
> Var(tmp)
[1] 0.9007241
>
> rowMeans(tmp)
[1] -0.06412957
> rowSums(tmp)
[1] -6.412957
> rowVars(tmp)
[1] 0.9007241
> rowSd(tmp)
[1] 0.9490649
> rowMax(tmp)
[1] 2.170585
> rowMin(tmp)
[1] -3.096631
>
> colMeans(tmp)
[1] 0.851350084 -0.773175184 -0.108030754 -1.072125545 -0.217147106
[6] -0.338227523 0.045526316 0.520868113 -0.621087197 1.216738073
[11] -0.624136709 -1.931659782 -0.152033105 1.088060538 -0.557526838
[16] 0.462599206 -0.864774103 0.569924701 0.815422371 -0.498574347
[21] -1.088355934 -0.516278293 -0.934673558 0.255451783 -0.126561583
[26] 0.417683319 0.564104508 -2.072834116 2.170584543 -0.605934436
[31] 0.014671428 0.038540591 1.559083934 1.131377865 -1.268990963
[36] 0.462967702 0.255759941 0.463443965 0.843213391 1.553618799
[41] 0.003553243 0.806734275 -0.987036398 -0.914287019 0.297150227
[46] 0.505752002 0.437672451 -1.002250194 0.658009992 0.589209624
[51] -0.889733436 -0.881745812 0.174588034 0.902053324 -0.440620257
[56] 1.181747959 -1.871978895 -0.091613005 -1.170595387 1.425490489
[61] -0.272205554 0.956614589 -0.083143782 0.292294916 -0.101023623
[66] 0.392667576 0.284997887 0.729099855 -2.303189621 -0.364678490
[71] -0.183037294 0.649054046 -0.855007404 1.160906312 -0.217829574
[76] -0.261283902 -1.293169963 0.345335375 -3.096631306 -0.208455880
[81] -1.330079018 0.721088885 0.946449008 0.289274911 -0.231409209
[86] 0.979114951 -0.122853417 -2.067661148 1.229704213 0.812897694
[91] -0.515075319 0.357131130 0.064509801 1.323285241 -0.904727015
[96] -1.599904937 -0.760889699 -0.512549510 -1.030377169 0.706834083
> colSums(tmp)
[1] 0.851350084 -0.773175184 -0.108030754 -1.072125545 -0.217147106
[6] -0.338227523 0.045526316 0.520868113 -0.621087197 1.216738073
[11] -0.624136709 -1.931659782 -0.152033105 1.088060538 -0.557526838
[16] 0.462599206 -0.864774103 0.569924701 0.815422371 -0.498574347
[21] -1.088355934 -0.516278293 -0.934673558 0.255451783 -0.126561583
[26] 0.417683319 0.564104508 -2.072834116 2.170584543 -0.605934436
[31] 0.014671428 0.038540591 1.559083934 1.131377865 -1.268990963
[36] 0.462967702 0.255759941 0.463443965 0.843213391 1.553618799
[41] 0.003553243 0.806734275 -0.987036398 -0.914287019 0.297150227
[46] 0.505752002 0.437672451 -1.002250194 0.658009992 0.589209624
[51] -0.889733436 -0.881745812 0.174588034 0.902053324 -0.440620257
[56] 1.181747959 -1.871978895 -0.091613005 -1.170595387 1.425490489
[61] -0.272205554 0.956614589 -0.083143782 0.292294916 -0.101023623
[66] 0.392667576 0.284997887 0.729099855 -2.303189621 -0.364678490
[71] -0.183037294 0.649054046 -0.855007404 1.160906312 -0.217829574
[76] -0.261283902 -1.293169963 0.345335375 -3.096631306 -0.208455880
[81] -1.330079018 0.721088885 0.946449008 0.289274911 -0.231409209
[86] 0.979114951 -0.122853417 -2.067661148 1.229704213 0.812897694
[91] -0.515075319 0.357131130 0.064509801 1.323285241 -0.904727015
[96] -1.599904937 -0.760889699 -0.512549510 -1.030377169 0.706834083
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] 0.851350084 -0.773175184 -0.108030754 -1.072125545 -0.217147106
[6] -0.338227523 0.045526316 0.520868113 -0.621087197 1.216738073
[11] -0.624136709 -1.931659782 -0.152033105 1.088060538 -0.557526838
[16] 0.462599206 -0.864774103 0.569924701 0.815422371 -0.498574347
[21] -1.088355934 -0.516278293 -0.934673558 0.255451783 -0.126561583
[26] 0.417683319 0.564104508 -2.072834116 2.170584543 -0.605934436
[31] 0.014671428 0.038540591 1.559083934 1.131377865 -1.268990963
[36] 0.462967702 0.255759941 0.463443965 0.843213391 1.553618799
[41] 0.003553243 0.806734275 -0.987036398 -0.914287019 0.297150227
[46] 0.505752002 0.437672451 -1.002250194 0.658009992 0.589209624
[51] -0.889733436 -0.881745812 0.174588034 0.902053324 -0.440620257
[56] 1.181747959 -1.871978895 -0.091613005 -1.170595387 1.425490489
[61] -0.272205554 0.956614589 -0.083143782 0.292294916 -0.101023623
[66] 0.392667576 0.284997887 0.729099855 -2.303189621 -0.364678490
[71] -0.183037294 0.649054046 -0.855007404 1.160906312 -0.217829574
[76] -0.261283902 -1.293169963 0.345335375 -3.096631306 -0.208455880
[81] -1.330079018 0.721088885 0.946449008 0.289274911 -0.231409209
[86] 0.979114951 -0.122853417 -2.067661148 1.229704213 0.812897694
[91] -0.515075319 0.357131130 0.064509801 1.323285241 -0.904727015
[96] -1.599904937 -0.760889699 -0.512549510 -1.030377169 0.706834083
> colMin(tmp)
[1] 0.851350084 -0.773175184 -0.108030754 -1.072125545 -0.217147106
[6] -0.338227523 0.045526316 0.520868113 -0.621087197 1.216738073
[11] -0.624136709 -1.931659782 -0.152033105 1.088060538 -0.557526838
[16] 0.462599206 -0.864774103 0.569924701 0.815422371 -0.498574347
[21] -1.088355934 -0.516278293 -0.934673558 0.255451783 -0.126561583
[26] 0.417683319 0.564104508 -2.072834116 2.170584543 -0.605934436
[31] 0.014671428 0.038540591 1.559083934 1.131377865 -1.268990963
[36] 0.462967702 0.255759941 0.463443965 0.843213391 1.553618799
[41] 0.003553243 0.806734275 -0.987036398 -0.914287019 0.297150227
[46] 0.505752002 0.437672451 -1.002250194 0.658009992 0.589209624
[51] -0.889733436 -0.881745812 0.174588034 0.902053324 -0.440620257
[56] 1.181747959 -1.871978895 -0.091613005 -1.170595387 1.425490489
[61] -0.272205554 0.956614589 -0.083143782 0.292294916 -0.101023623
[66] 0.392667576 0.284997887 0.729099855 -2.303189621 -0.364678490
[71] -0.183037294 0.649054046 -0.855007404 1.160906312 -0.217829574
[76] -0.261283902 -1.293169963 0.345335375 -3.096631306 -0.208455880
[81] -1.330079018 0.721088885 0.946449008 0.289274911 -0.231409209
[86] 0.979114951 -0.122853417 -2.067661148 1.229704213 0.812897694
[91] -0.515075319 0.357131130 0.064509801 1.323285241 -0.904727015
[96] -1.599904937 -0.760889699 -0.512549510 -1.030377169 0.706834083
> colMedians(tmp)
[1] 0.851350084 -0.773175184 -0.108030754 -1.072125545 -0.217147106
[6] -0.338227523 0.045526316 0.520868113 -0.621087197 1.216738073
[11] -0.624136709 -1.931659782 -0.152033105 1.088060538 -0.557526838
[16] 0.462599206 -0.864774103 0.569924701 0.815422371 -0.498574347
[21] -1.088355934 -0.516278293 -0.934673558 0.255451783 -0.126561583
[26] 0.417683319 0.564104508 -2.072834116 2.170584543 -0.605934436
[31] 0.014671428 0.038540591 1.559083934 1.131377865 -1.268990963
[36] 0.462967702 0.255759941 0.463443965 0.843213391 1.553618799
[41] 0.003553243 0.806734275 -0.987036398 -0.914287019 0.297150227
[46] 0.505752002 0.437672451 -1.002250194 0.658009992 0.589209624
[51] -0.889733436 -0.881745812 0.174588034 0.902053324 -0.440620257
[56] 1.181747959 -1.871978895 -0.091613005 -1.170595387 1.425490489
[61] -0.272205554 0.956614589 -0.083143782 0.292294916 -0.101023623
[66] 0.392667576 0.284997887 0.729099855 -2.303189621 -0.364678490
[71] -0.183037294 0.649054046 -0.855007404 1.160906312 -0.217829574
[76] -0.261283902 -1.293169963 0.345335375 -3.096631306 -0.208455880
[81] -1.330079018 0.721088885 0.946449008 0.289274911 -0.231409209
[86] 0.979114951 -0.122853417 -2.067661148 1.229704213 0.812897694
[91] -0.515075319 0.357131130 0.064509801 1.323285241 -0.904727015
[96] -1.599904937 -0.760889699 -0.512549510 -1.030377169 0.706834083
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.8513501 -0.7731752 -0.1080308 -1.072126 -0.2171471 -0.3382275 0.04552632
[2,] 0.8513501 -0.7731752 -0.1080308 -1.072126 -0.2171471 -0.3382275 0.04552632
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.5208681 -0.6210872 1.216738 -0.6241367 -1.93166 -0.1520331 1.088061
[2,] 0.5208681 -0.6210872 1.216738 -0.6241367 -1.93166 -0.1520331 1.088061
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.5575268 0.4625992 -0.8647741 0.5699247 0.8154224 -0.4985743 -1.088356
[2,] -0.5575268 0.4625992 -0.8647741 0.5699247 0.8154224 -0.4985743 -1.088356
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.5162783 -0.9346736 0.2554518 -0.1265616 0.4176833 0.5641045 -2.072834
[2,] -0.5162783 -0.9346736 0.2554518 -0.1265616 0.4176833 0.5641045 -2.072834
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 2.170585 -0.6059344 0.01467143 0.03854059 1.559084 1.131378 -1.268991
[2,] 2.170585 -0.6059344 0.01467143 0.03854059 1.559084 1.131378 -1.268991
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.4629677 0.2557599 0.463444 0.8432134 1.553619 0.003553243 0.8067343
[2,] 0.4629677 0.2557599 0.463444 0.8432134 1.553619 0.003553243 0.8067343
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.9870364 -0.914287 0.2971502 0.505752 0.4376725 -1.00225 0.65801
[2,] -0.9870364 -0.914287 0.2971502 0.505752 0.4376725 -1.00225 0.65801
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.5892096 -0.8897334 -0.8817458 0.174588 0.9020533 -0.4406203 1.181748
[2,] 0.5892096 -0.8897334 -0.8817458 0.174588 0.9020533 -0.4406203 1.181748
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.871979 -0.09161301 -1.170595 1.42549 -0.2722056 0.9566146 -0.08314378
[2,] -1.871979 -0.09161301 -1.170595 1.42549 -0.2722056 0.9566146 -0.08314378
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.2922949 -0.1010236 0.3926676 0.2849979 0.7290999 -2.30319 -0.3646785
[2,] 0.2922949 -0.1010236 0.3926676 0.2849979 0.7290999 -2.30319 -0.3646785
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.1830373 0.649054 -0.8550074 1.160906 -0.2178296 -0.2612839 -1.29317
[2,] -0.1830373 0.649054 -0.8550074 1.160906 -0.2178296 -0.2612839 -1.29317
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.3453354 -3.096631 -0.2084559 -1.330079 0.7210889 0.946449 0.2892749
[2,] 0.3453354 -3.096631 -0.2084559 -1.330079 0.7210889 0.946449 0.2892749
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.2314092 0.979115 -0.1228534 -2.067661 1.229704 0.8128977 -0.5150753
[2,] -0.2314092 0.979115 -0.1228534 -2.067661 1.229704 0.8128977 -0.5150753
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.3571311 0.0645098 1.323285 -0.904727 -1.599905 -0.7608897 -0.5125495
[2,] 0.3571311 0.0645098 1.323285 -0.904727 -1.599905 -0.7608897 -0.5125495
[,99] [,100]
[1,] -1.030377 0.7068341
[2,] -1.030377 0.7068341
>
>
> Max(tmp2)
[1] 2.55467
> Min(tmp2)
[1] -2.581776
> mean(tmp2)
[1] 0.116176
> Sum(tmp2)
[1] 11.6176
> Var(tmp2)
[1] 1.251632
>
> rowMeans(tmp2)
[1] 0.748543383 1.956874591 0.458280287 2.554670363 0.319285429
[6] -0.248208889 0.809548252 1.811003526 0.056573923 -0.072694524
[11] -1.429683893 -1.039500141 1.657312441 -1.521379071 -0.776304618
[16] -0.488322563 -0.999625237 -0.906260149 1.550044611 1.055710341
[21] -1.003753920 -1.131384855 0.275795847 -1.023532198 0.217154036
[26] -0.194927309 0.100429151 1.921788194 -0.925014929 0.205478999
[31] -2.540996564 0.206746086 -0.822011401 1.748433650 0.944064270
[36] -1.102957707 0.278160953 0.986426668 1.647813819 0.028851496
[41] 0.240130811 0.689121286 -0.023279126 -2.315003857 -0.951630926
[46] 0.382796380 -1.676406462 0.056938087 1.977967216 0.408103842
[51] 1.085226319 0.015369938 -0.826759077 -0.113518230 1.730119277
[56] 0.616691946 0.484458750 0.085640698 -0.150391680 1.019263336
[61] 1.225428572 0.312636098 -1.156878738 0.370803602 0.784124001
[66] -1.223855815 -0.216763454 2.211755470 0.727396230 -1.852511848
[71] 1.031376932 -1.080476735 0.990073496 -1.464450586 0.586319600
[76] -0.155819780 1.572770751 -0.496797528 0.100659687 -0.673488616
[81] 0.001739746 -2.581776286 -0.753072831 2.140629775 0.304341160
[86] 0.291149404 -0.130852692 -0.510454099 -1.839112371 1.627056491
[91] -1.240197050 0.176984632 0.349141776 0.014825789 1.942442735
[96] -0.454293899 1.031977959 0.038113896 1.735045394 -0.165660399
> rowSums(tmp2)
[1] 0.748543383 1.956874591 0.458280287 2.554670363 0.319285429
[6] -0.248208889 0.809548252 1.811003526 0.056573923 -0.072694524
[11] -1.429683893 -1.039500141 1.657312441 -1.521379071 -0.776304618
[16] -0.488322563 -0.999625237 -0.906260149 1.550044611 1.055710341
[21] -1.003753920 -1.131384855 0.275795847 -1.023532198 0.217154036
[26] -0.194927309 0.100429151 1.921788194 -0.925014929 0.205478999
[31] -2.540996564 0.206746086 -0.822011401 1.748433650 0.944064270
[36] -1.102957707 0.278160953 0.986426668 1.647813819 0.028851496
[41] 0.240130811 0.689121286 -0.023279126 -2.315003857 -0.951630926
[46] 0.382796380 -1.676406462 0.056938087 1.977967216 0.408103842
[51] 1.085226319 0.015369938 -0.826759077 -0.113518230 1.730119277
[56] 0.616691946 0.484458750 0.085640698 -0.150391680 1.019263336
[61] 1.225428572 0.312636098 -1.156878738 0.370803602 0.784124001
[66] -1.223855815 -0.216763454 2.211755470 0.727396230 -1.852511848
[71] 1.031376932 -1.080476735 0.990073496 -1.464450586 0.586319600
[76] -0.155819780 1.572770751 -0.496797528 0.100659687 -0.673488616
[81] 0.001739746 -2.581776286 -0.753072831 2.140629775 0.304341160
[86] 0.291149404 -0.130852692 -0.510454099 -1.839112371 1.627056491
[91] -1.240197050 0.176984632 0.349141776 0.014825789 1.942442735
[96] -0.454293899 1.031977959 0.038113896 1.735045394 -0.165660399
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 0.748543383 1.956874591 0.458280287 2.554670363 0.319285429
[6] -0.248208889 0.809548252 1.811003526 0.056573923 -0.072694524
[11] -1.429683893 -1.039500141 1.657312441 -1.521379071 -0.776304618
[16] -0.488322563 -0.999625237 -0.906260149 1.550044611 1.055710341
[21] -1.003753920 -1.131384855 0.275795847 -1.023532198 0.217154036
[26] -0.194927309 0.100429151 1.921788194 -0.925014929 0.205478999
[31] -2.540996564 0.206746086 -0.822011401 1.748433650 0.944064270
[36] -1.102957707 0.278160953 0.986426668 1.647813819 0.028851496
[41] 0.240130811 0.689121286 -0.023279126 -2.315003857 -0.951630926
[46] 0.382796380 -1.676406462 0.056938087 1.977967216 0.408103842
[51] 1.085226319 0.015369938 -0.826759077 -0.113518230 1.730119277
[56] 0.616691946 0.484458750 0.085640698 -0.150391680 1.019263336
[61] 1.225428572 0.312636098 -1.156878738 0.370803602 0.784124001
[66] -1.223855815 -0.216763454 2.211755470 0.727396230 -1.852511848
[71] 1.031376932 -1.080476735 0.990073496 -1.464450586 0.586319600
[76] -0.155819780 1.572770751 -0.496797528 0.100659687 -0.673488616
[81] 0.001739746 -2.581776286 -0.753072831 2.140629775 0.304341160
[86] 0.291149404 -0.130852692 -0.510454099 -1.839112371 1.627056491
[91] -1.240197050 0.176984632 0.349141776 0.014825789 1.942442735
[96] -0.454293899 1.031977959 0.038113896 1.735045394 -0.165660399
> rowMin(tmp2)
[1] 0.748543383 1.956874591 0.458280287 2.554670363 0.319285429
[6] -0.248208889 0.809548252 1.811003526 0.056573923 -0.072694524
[11] -1.429683893 -1.039500141 1.657312441 -1.521379071 -0.776304618
[16] -0.488322563 -0.999625237 -0.906260149 1.550044611 1.055710341
[21] -1.003753920 -1.131384855 0.275795847 -1.023532198 0.217154036
[26] -0.194927309 0.100429151 1.921788194 -0.925014929 0.205478999
[31] -2.540996564 0.206746086 -0.822011401 1.748433650 0.944064270
[36] -1.102957707 0.278160953 0.986426668 1.647813819 0.028851496
[41] 0.240130811 0.689121286 -0.023279126 -2.315003857 -0.951630926
[46] 0.382796380 -1.676406462 0.056938087 1.977967216 0.408103842
[51] 1.085226319 0.015369938 -0.826759077 -0.113518230 1.730119277
[56] 0.616691946 0.484458750 0.085640698 -0.150391680 1.019263336
[61] 1.225428572 0.312636098 -1.156878738 0.370803602 0.784124001
[66] -1.223855815 -0.216763454 2.211755470 0.727396230 -1.852511848
[71] 1.031376932 -1.080476735 0.990073496 -1.464450586 0.586319600
[76] -0.155819780 1.572770751 -0.496797528 0.100659687 -0.673488616
[81] 0.001739746 -2.581776286 -0.753072831 2.140629775 0.304341160
[86] 0.291149404 -0.130852692 -0.510454099 -1.839112371 1.627056491
[91] -1.240197050 0.176984632 0.349141776 0.014825789 1.942442735
[96] -0.454293899 1.031977959 0.038113896 1.735045394 -0.165660399
>
> colMeans(tmp2)
[1] 0.116176
> colSums(tmp2)
[1] 11.6176
> colVars(tmp2)
[1] 1.251632
> colSd(tmp2)
[1] 1.118764
> colMax(tmp2)
[1] 2.55467
> colMin(tmp2)
[1] -2.581776
> colMedians(tmp2)
[1] 0.1005444
> colRanges(tmp2)
[,1]
[1,] -2.581776
[2,] 2.554670
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.8818348 -5.2827926 3.0685958 -1.5738768 0.1326297 -6.6326846
[7] 1.1168222 1.5992780 0.6878837 2.0135298
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.2059405
[2,] -0.3210839
[3,] 0.3503324
[4,] 0.7366877
[5,] 2.5747217
>
> rowApply(tmp,sum)
[1] -0.9788021 3.9078420 -2.8517129 -6.9638762 1.3118463 3.1162343
[7] 1.4864466 2.9064281 -2.1051620 -1.8180240
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 2 7 7 4 5 10 6 7 8 3
[2,] 4 1 6 3 10 1 3 4 1 6
[3,] 6 10 10 1 3 7 2 3 10 9
[4,] 3 9 5 8 6 8 4 2 2 4
[5,] 1 5 9 6 8 2 10 9 7 1
[6,] 7 8 1 7 1 4 7 1 3 2
[7,] 10 4 3 10 2 5 5 6 6 10
[8,] 9 6 4 5 7 3 9 8 4 7
[9,] 5 3 2 2 4 6 8 10 9 8
[10,] 8 2 8 9 9 9 1 5 5 5
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.8697495 2.7757558 -0.4509012 -2.7114577 1.6221592 -2.2833883
[7] -4.9667677 1.4045445 1.1419668 2.2595064 -1.1242554 0.3335542
[13] -0.7920481 1.8621312 -2.0716148 2.5033021 0.5765934 1.4627670
[19] 1.0477285 -0.5184155
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.2238269
[2,] -0.1944823
[3,] 0.1007916
[4,] 0.5387597
[5,] 0.6485074
>
> rowApply(tmp,sum)
[1] 13.082252 -2.815993 -1.657476 -10.000881 4.333008
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 9 17 13 13 5
[2,] 18 15 18 10 13
[3,] 2 18 9 9 8
[4,] 12 7 10 12 1
[5,] 11 10 16 19 9
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.5387597 1.5988024 -0.6114494 0.78712865 0.7761971 -1.3103086
[2,] 0.6485074 0.3471774 0.8110602 -0.59939443 -0.4027908 -1.0557158
[3,] 0.1007916 0.9479984 -0.1295902 -0.07793237 0.3345364 -0.9393069
[4,] -0.2238269 -0.5577443 -0.6663053 -0.27405061 0.7155696 -0.4456721
[5,] -0.1944823 0.4395218 0.1453836 -2.54720891 0.1986469 1.4676151
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.1593518 -0.11073771 1.58896153 0.4130851 1.725273345 -0.09293476
[2,] -0.3897256 -0.02354043 0.07411019 -0.7647582 -0.900638106 1.00794673
[3,] -1.2690498 0.33242444 -0.14147062 2.0919902 -0.739241487 0.01517137
[4,] -1.1121689 0.32059428 -1.93813514 -0.8905793 -1.211409189 -1.13768166
[5,] -2.0364716 0.88580396 1.55850080 1.4097685 0.001760069 0.54105249
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.2434438 1.3006919 -0.14072578 0.9686891 1.1447909 2.42379953
[2,] -0.4689214 0.3312099 -0.71523424 -0.5273886 0.5729557 0.95548758
[3,] -1.1181301 -1.0561600 -1.43610298 -0.6651534 0.1678257 0.06952882
[4,] 0.3325751 -0.2035628 -0.06162408 1.2540781 -1.6233312 -1.18222819
[5,] 0.2189845 1.4899522 0.28207226 1.4730768 0.3143523 -0.80382079
[,19] [,20]
[1,] 1.3621781 0.63595899
[2,] -0.8230977 -0.89324317
[3,] 0.6092109 1.24518444
[4,] 0.4275792 -1.52295795
[5,] -0.5281420 0.01664214
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 649 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 563 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 1.741582 -0.3650305 0.2937142 -0.9222754 0.4282224 -0.1387411 -2.113948
col8 col9 col10 col11 col12 col13 col14
row1 0.7872463 0.3837894 0.09648359 -0.7863867 0.05263784 0.6425727 -0.3889275
col15 col16 col17 col18 col19 col20
row1 -0.1152255 -0.0744338 -0.04521006 0.362904 -0.7554803 -1.622384
> tmp[,"col10"]
col10
row1 0.09648359
row2 1.60556172
row3 0.85355464
row4 -0.78066675
row5 -0.08421466
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.7415823 -0.3650305 0.2937142 -0.9222754 0.4282224 -0.1387411 -2.113948
row5 0.4539578 -1.5042757 1.8345445 0.4475817 1.6914117 -1.6527053 -1.943589
col8 col9 col10 col11 col12 col13
row1 0.787246257 0.3837894 0.09648359 -0.7863867 0.05263784 0.6425727
row5 0.004795045 -0.5608710 -0.08421466 -1.1111867 0.08995046 0.0840010
col14 col15 col16 col17 col18 col19
row1 -0.3889275 -0.1152255 -0.0744338 -0.04521006 0.362904 -0.7554803
row5 1.4151935 1.5680767 -1.1637891 -0.60619611 1.244247 -0.4675814
col20
row1 -1.622383594
row5 0.003369259
> tmp[,c("col6","col20")]
col6 col20
row1 -0.1387411 -1.622383594
row2 0.1187563 0.071452639
row3 0.2531555 -2.092161906
row4 -1.3207267 -0.061195113
row5 -1.6527053 0.003369259
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.1387411 -1.622383594
row5 -1.6527053 0.003369259
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.37678 49.72288 49.60653 49.45144 50.12955 104.4159 47.35473 50.92645
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.41861 49.39408 51.33086 48.45861 49.0632 49.0204 50.93813 51.58084
col17 col18 col19 col20
row1 50.51252 48.8186 51.2092 105.7419
> tmp[,"col10"]
col10
row1 49.39408
row2 29.85233
row3 29.05811
row4 29.57922
row5 51.84629
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.37678 49.72288 49.60653 49.45144 50.12955 104.4159 47.35473 50.92645
row5 51.24743 49.79229 51.32459 49.45018 52.31696 103.6999 50.65900 49.08652
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.41861 49.39408 51.33086 48.45861 49.06320 49.02040 50.93813 51.58084
row5 49.18791 51.84629 49.60040 49.84606 48.70852 48.30909 48.96758 51.71205
col17 col18 col19 col20
row1 50.51252 48.81860 51.20920 105.7419
row5 50.17638 48.27496 50.89199 103.6896
> tmp[,c("col6","col20")]
col6 col20
row1 104.41587 105.74187
row2 75.23117 75.26085
row3 74.11774 75.84329
row4 76.50479 76.26181
row5 103.69993 103.68962
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.4159 105.7419
row5 103.6999 103.6896
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.4159 105.7419
row5 103.6999 103.6896
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -1.2739702
[2,] 0.0353954
[3,] 0.1833001
[4,] -0.4489272
[5,] -0.4147317
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.71465598 -0.8096337
[2,] -1.69403269 -0.7961269
[3,] -1.46111048 0.1913097
[4,] 0.02531627 -0.9483932
[5,] -0.11289006 1.0069195
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.03340197 1.2180818
[2,] 0.29135957 -1.2816087
[3,] 1.70198322 0.4639453
[4,] -0.47259622 -0.5863380
[5,] -0.32885705 0.6567471
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.03340197
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.03340197
[2,] 0.29135957
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -0.2478548 -1.4857209 1.2225386 0.7477159 -1.4543677 -0.7190219
row1 -0.4512600 0.5062024 -0.6608729 -0.4212654 0.2474094 1.5447165
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 0.1141033 -0.3924588 0.4102850 -0.8264898 -1.183637 -1.3294058 0.6541678
row1 2.1657663 -0.4308205 -0.6608902 -1.5233860 -1.446227 -0.3248234 0.2893622
[,14] [,15] [,16] [,17] [,18] [,19]
row3 -0.28079444 -0.29164914 1.3181927 0.5214222 -0.5045107 -0.8092195
row1 -0.03900645 -0.05202015 0.8489799 -0.8730704 0.8630699 -0.5540261
[,20]
row3 -0.3446110
row1 0.5924331
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.069925 0.08116776 0.9658302 -0.7410633 0.3848497 0.5287363 0.1276358
[,8] [,9] [,10]
row2 -0.7780668 0.4969345 0.1263987
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.2065198 -1.336286 0.8012812 -0.2556087 1.25065 -1.813914 -0.01545781
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.9658621 0.3605764 0.495883 0.2577812 -1.497961 2.29292 0.293942
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.296809 -0.5298203 -0.3976946 0.7728976 -1.020379 -0.5532748
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x60000113c000>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf85b2923d"
[2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf8e9ee5b7"
[3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf861fb58e0"
[4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf83c880c61"
[5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf87e4d353"
[6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf83fedf231"
[7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf81eb78fc1"
[8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf8253ed7a8"
[9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf840c069b2"
[10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf8185b4654"
[11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf81066414a"
[12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf8294869af"
[13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf851127555"
[14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf812d54908"
[15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMdbf870adb5e0"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x600001144120>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x600001144120>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x600001144120>
> rowMedians(tmp)
[1] -0.176749281 0.355636816 -0.041247883 -0.316213828 0.230649412
[6] -0.409343818 0.124705099 0.159492399 -0.138415664 -0.011039276
[11] -0.197793311 0.463337161 -0.376070085 0.244020881 0.368660053
[16] 0.150384243 0.556778006 -0.482329755 -0.237979045 -0.426588467
[21] -0.139375883 -0.061252620 0.290656788 0.356965017 -0.078229445
[26] 0.089717076 -0.647723137 -0.085613874 0.012103706 0.110838281
[31] -0.442102452 0.310715312 -0.520776615 0.100718426 -0.087332635
[36] 0.228746020 0.396591750 0.364247370 -0.042234937 0.583116875
[41] -0.115623390 0.120807751 -0.089858757 -0.467927269 -0.547277517
[46] 0.292287450 0.124120707 0.016065157 -0.218417396 -0.123573585
[51] -0.116659403 0.021195031 -0.283419287 -0.007630178 -0.030710055
[56] 0.254987782 0.155589406 0.267196924 -0.218893984 0.826871191
[61] 0.094544584 -0.362600083 -0.450821333 -0.445437325 -0.035129643
[66] 0.016373381 0.144926709 0.086578080 0.342450031 -0.034337692
[71] -0.132075442 -0.552397398 -0.065827944 -0.060913383 0.018531336
[76] -0.500272637 0.151054149 0.015053358 0.530513619 0.152862788
[81] -0.078989107 -0.278732876 -0.119820477 0.270730058 -0.188734621
[86] -0.558394277 -0.156183084 -0.641123725 -0.273192958 -0.544376768
[91] -0.296617140 0.042580717 0.336293940 0.193023110 0.177058777
[96] -0.245877244 -0.039634378 -0.415876688 0.125875053 0.014989421
[101] 0.136069039 0.185345334 -0.352125141 0.033909881 -0.209221422
[106] 0.075769550 0.496129133 -0.337108179 0.097151822 0.066019072
[111] 0.549588145 0.542356327 -0.488168876 -0.007884771 -0.827886818
[116] -0.374766916 0.307552019 0.538949028 0.109715673 0.090092364
[121] -0.034335312 0.240402980 -0.355568639 -0.198846437 0.027611425
[126] 0.039039412 -0.171120217 0.433719004 -0.417617487 -0.071085611
[131] 0.329269510 -0.073271217 0.108011652 0.016911963 0.022569096
[136] 0.508769544 -0.057299475 0.355629209 0.397824156 0.059677091
[141] -0.050260528 0.020381429 0.419865773 -0.063862349 0.503326031
[146] 0.083659560 -0.042127166 0.490424388 -0.423572729 -0.033987343
[151] -0.024617271 0.290920366 -0.477216436 -0.160619985 -0.198693601
[156] -0.460075697 0.377242884 -0.005087829 -0.014617978 0.544556548
[161] -0.524387320 0.672364740 -0.207851655 -0.311060626 0.202761823
[166] -0.722793776 -0.180469859 -0.493022402 -0.165328056 0.508658951
[171] -0.379076208 -0.287674917 -0.412322507 0.351440573 0.363141159
[176] 0.297606834 0.122287861 -0.109468376 0.352781584 0.196291004
[181] 0.009763991 0.329829241 0.062679729 0.461626538 0.119718329
[186] -0.193811668 -0.308772283 -0.194606429 0.208015241 0.512675558
[191] 0.432527841 0.259737959 -0.012687072 -0.428584442 -0.706653818
[196] 0.129157232 0.149468030 -0.237872982 -0.433127179 -0.037205912
[201] -0.122800187 -0.094071119 -0.274787958 -0.228713144 0.272083938
[206] 0.340662842 -0.283777981 0.579497673 0.153757892 -0.043644182
[211] -0.307904767 0.334425761 -0.160552920 -0.469378886 -0.374320074
[216] -0.128487411 0.434520916 0.330269710 0.098881804 -0.206397850
[221] -0.499369415 0.332648588 -0.268950048 -0.055842049 -0.115590599
[226] -0.194107021 -0.500562019 -0.123322467 -0.085851325 -0.325653219
>
> proc.time()
user system elapsed
5.044 18.716 26.711
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003188000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003188000>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003188000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x600003188000>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x600003188300>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003188300>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x600003188300>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003188300>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003188300>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003180000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003180000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003180000>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003180000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003180000>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600003180000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003180000>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600003180000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003180000>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031fc000>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x6000031fc000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031fc000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031fc000>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilee0fe34e2da6a" "BufferedMatrixFilee0fe7b615c0e"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilee0fe34e2da6a" "BufferedMatrixFilee0fe7b615c0e"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031fc240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031fc240>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000031fc240>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000031fc240>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6000031fc240>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6000031fc240>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031fc420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000031fc420>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000031fc420>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x6000031fc420>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x60000318c1e0>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x60000318c1e0>
> rm(P)
>
> proc.time()
user system elapsed
0.587 0.212 0.987
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.563 0.130 0.669