Ben Bolstad
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: 0147962 |
| git_last_commit_date: 2025-04-15 09:39:39 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 252/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.73.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.73.0 |
| 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_1.73.0.tar.gz |
| StartedAt: 2025-08-29 19:35:08 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 19:35:57 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 49.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.73.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.73.0’
* 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.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 ‘1.73.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.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 4.5.1 (2025-06-13) -- "Great Square Root"
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
0.332 0.144 0.472
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
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 480847 25.7 1056617 56.5 NA 634462 33.9
Vcells 891074 6.8 8388608 64.0 98304 2108713 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 Aug 29 19:35:31 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 Aug 29 19:35:32 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: 0x600000a08000>
>
>
>
> 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 Aug 29 19:35:36 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 Aug 29 19:35:38 2025"
>
> ColMode(tmp2)
<pointer: 0x600000a08000>
>
>
>
> ### 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,] 98.9012609 0.3229283 0.3533640 0.6866212
[2,] -0.6913758 0.9194574 2.1454452 -1.7616756
[3,] -0.4382837 -0.1010353 -2.2523231 -0.5313966
[4,] -1.0917815 -1.1191207 0.1418084 -1.1572052
> 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,] 98.9012609 0.3229283 0.3533640 0.6866212
[2,] 0.6913758 0.9194574 2.1454452 1.7616756
[3,] 0.4382837 0.1010353 2.2523231 0.5313966
[4,] 1.0917815 1.1191207 0.1418084 1.1572052
> 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,] 9.9449113 0.5682678 0.5944443 0.8286261
[2,] 0.8314901 0.9588834 1.4647338 1.3272813
[3,] 0.6620300 0.3178605 1.5007742 0.7289695
[4,] 1.0448835 1.0578850 0.3765746 1.0757347
>
> 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,] 223.35037 31.00561 31.29781 33.97288
[2,] 34.00628 35.50829 41.79278 40.03449
[3,] 32.05858 28.27964 42.26006 32.82109
[4,] 36.54062 36.69797 28.90755 36.91455
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600000a74120>
> exp(tmp5)
<pointer: 0x600000a74120>
> log(tmp5,2)
<pointer: 0x600000a74120>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 464.8745
> Min(tmp5)
[1] 53.86056
> mean(tmp5)
[1] 72.76015
> Sum(tmp5)
[1] 14552.03
> Var(tmp5)
[1] 845.9637
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.51757 71.42959 71.07248 71.59452 71.78778 69.42486 69.73428 72.48282
[9] 69.16415 69.39342
> rowSums(tmp5)
[1] 1830.351 1428.592 1421.450 1431.890 1435.756 1388.497 1394.686 1449.656
[9] 1383.283 1387.868
> rowVars(tmp5)
[1] 7787.86784 80.12150 79.33344 63.84355 103.14952 87.57861
[7] 38.08450 73.79819 59.69953 62.26286
> rowSd(tmp5)
[1] 88.248897 8.951062 8.906932 7.990216 10.156255 9.358344 6.171264
[8] 8.590587 7.726547 7.890682
> rowMax(tmp5)
[1] 464.87454 86.98620 87.95879 88.36749 90.82096 92.59649 81.34034
[8] 89.83636 83.23877 83.05316
> rowMin(tmp5)
[1] 59.02383 54.87424 58.86037 54.04213 53.86056 56.13214 57.26452 55.90518
[9] 54.93731 54.03180
>
> colMeans(tmp5)
[1] 109.01763 67.09058 70.57750 69.72795 71.89574 72.94072 73.03790
[8] 69.63582 70.34306 71.13550 74.31648 72.28655 70.41926 72.14446
[15] 74.12815 67.70393 74.87156 67.97462 65.74226 70.21330
> colSums(tmp5)
[1] 1090.1763 670.9058 705.7750 697.2795 718.9574 729.4072 730.3790
[8] 696.3582 703.4306 711.3550 743.1648 722.8655 704.1926 721.4446
[15] 741.2815 677.0393 748.7156 679.7462 657.4226 702.1330
> colVars(tmp5)
[1] 15723.45854 64.02311 107.66741 134.69774 24.01738 26.96753
[7] 87.79156 111.21912 90.72126 30.23981 62.50583 43.84243
[13] 49.31585 109.32247 97.89518 59.31743 83.51889 54.95102
[19] 51.51446 26.82722
> colSd(tmp5)
[1] 125.393216 8.001444 10.376291 11.605936 4.900753 5.193027
[7] 9.369715 10.546048 9.524771 5.499073 7.906063 6.621362
[13] 7.022524 10.455739 9.894199 7.701781 9.138867 7.412896
[19] 7.177357 5.179500
> colMax(tmp5)
[1] 464.87454 79.03472 87.95879 89.83636 80.33266 81.29755 85.07278
[8] 85.19666 92.59649 83.23877 83.24003 80.92623 80.60989 90.73350
[15] 88.36749 83.14058 88.15749 85.37682 78.96279 77.29470
> colMin(tmp5)
[1] 57.26452 57.70167 54.93731 53.86056 64.45007 65.15124 55.90518 54.04213
[9] 54.03180 65.28280 63.28980 62.74779 61.02095 58.25259 59.66916 54.87424
[17] 59.12766 60.68253 57.41988 61.52291
>
>
> ### 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] 91.51757 71.42959 71.07248 71.59452 71.78778 69.42486 69.73428 72.48282
[9] 69.16415 NA
> rowSums(tmp5)
[1] 1830.351 1428.592 1421.450 1431.890 1435.756 1388.497 1394.686 1449.656
[9] 1383.283 NA
> rowVars(tmp5)
[1] 7787.86784 80.12150 79.33344 63.84355 103.14952 87.57861
[7] 38.08450 73.79819 59.69953 65.35114
> rowSd(tmp5)
[1] 88.248897 8.951062 8.906932 7.990216 10.156255 9.358344 6.171264
[8] 8.590587 7.726547 8.084005
> rowMax(tmp5)
[1] 464.87454 86.98620 87.95879 88.36749 90.82096 92.59649 81.34034
[8] 89.83636 83.23877 NA
> rowMin(tmp5)
[1] 59.02383 54.87424 58.86037 54.04213 53.86056 56.13214 57.26452 55.90518
[9] 54.93731 NA
>
> colMeans(tmp5)
[1] 109.01763 67.09058 70.57750 69.72795 71.89574 72.94072 73.03790
[8] 69.63582 70.34306 71.13550 74.31648 72.28655 70.41926 72.14446
[15] 74.12815 67.70393 74.87156 67.97462 65.74226 NA
> colSums(tmp5)
[1] 1090.1763 670.9058 705.7750 697.2795 718.9574 729.4072 730.3790
[8] 696.3582 703.4306 711.3550 743.1648 722.8655 704.1926 721.4446
[15] 741.2815 677.0393 748.7156 679.7462 657.4226 NA
> colVars(tmp5)
[1] 15723.45854 64.02311 107.66741 134.69774 24.01738 26.96753
[7] 87.79156 111.21912 90.72126 30.23981 62.50583 43.84243
[13] 49.31585 109.32247 97.89518 59.31743 83.51889 54.95102
[19] 51.51446 NA
> colSd(tmp5)
[1] 125.393216 8.001444 10.376291 11.605936 4.900753 5.193027
[7] 9.369715 10.546048 9.524771 5.499073 7.906063 6.621362
[13] 7.022524 10.455739 9.894199 7.701781 9.138867 7.412896
[19] 7.177357 NA
> colMax(tmp5)
[1] 464.87454 79.03472 87.95879 89.83636 80.33266 81.29755 85.07278
[8] 85.19666 92.59649 83.23877 83.24003 80.92623 80.60989 90.73350
[15] 88.36749 83.14058 88.15749 85.37682 78.96279 NA
> colMin(tmp5)
[1] 57.26452 57.70167 54.93731 53.86056 64.45007 65.15124 55.90518 54.04213
[9] 54.03180 65.28280 63.28980 62.74779 61.02095 58.25259 59.66916 54.87424
[17] 59.12766 60.68253 57.41988 NA
>
> Max(tmp5,na.rm=TRUE)
[1] 464.8745
> Min(tmp5,na.rm=TRUE)
[1] 53.86056
> mean(tmp5,na.rm=TRUE)
[1] 72.78972
> Sum(tmp5,na.rm=TRUE)
[1] 14485.15
> Var(tmp5,na.rm=TRUE)
[1] 850.0605
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.51757 71.42959 71.07248 71.59452 71.78778 69.42486 69.73428 72.48282
[9] 69.16415 69.52594
> rowSums(tmp5,na.rm=TRUE)
[1] 1830.351 1428.592 1421.450 1431.890 1435.756 1388.497 1394.686 1449.656
[9] 1383.283 1320.993
> rowVars(tmp5,na.rm=TRUE)
[1] 7787.86784 80.12150 79.33344 63.84355 103.14952 87.57861
[7] 38.08450 73.79819 59.69953 65.35114
> rowSd(tmp5,na.rm=TRUE)
[1] 88.248897 8.951062 8.906932 7.990216 10.156255 9.358344 6.171264
[8] 8.590587 7.726547 8.084005
> rowMax(tmp5,na.rm=TRUE)
[1] 464.87454 86.98620 87.95879 88.36749 90.82096 92.59649 81.34034
[8] 89.83636 83.23877 83.05316
> rowMin(tmp5,na.rm=TRUE)
[1] 59.02383 54.87424 58.86037 54.04213 53.86056 56.13214 57.26452 55.90518
[9] 54.93731 54.03180
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.01763 67.09058 70.57750 69.72795 71.89574 72.94072 73.03790
[8] 69.63582 70.34306 71.13550 74.31648 72.28655 70.41926 72.14446
[15] 74.12815 67.70393 74.87156 67.97462 65.74226 70.58417
> colSums(tmp5,na.rm=TRUE)
[1] 1090.1763 670.9058 705.7750 697.2795 718.9574 729.4072 730.3790
[8] 696.3582 703.4306 711.3550 743.1648 722.8655 704.1926 721.4446
[15] 741.2815 677.0393 748.7156 679.7462 657.4226 635.2575
> colVars(tmp5,na.rm=TRUE)
[1] 15723.45854 64.02311 107.66741 134.69774 24.01738 26.96753
[7] 87.79156 111.21912 90.72126 30.23981 62.50583 43.84243
[13] 49.31585 109.32247 97.89518 59.31743 83.51889 54.95102
[19] 51.51446 28.63324
> colSd(tmp5,na.rm=TRUE)
[1] 125.393216 8.001444 10.376291 11.605936 4.900753 5.193027
[7] 9.369715 10.546048 9.524771 5.499073 7.906063 6.621362
[13] 7.022524 10.455739 9.894199 7.701781 9.138867 7.412896
[19] 7.177357 5.351004
> colMax(tmp5,na.rm=TRUE)
[1] 464.87454 79.03472 87.95879 89.83636 80.33266 81.29755 85.07278
[8] 85.19666 92.59649 83.23877 83.24003 80.92623 80.60989 90.73350
[15] 88.36749 83.14058 88.15749 85.37682 78.96279 77.29470
> colMin(tmp5,na.rm=TRUE)
[1] 57.26452 57.70167 54.93731 53.86056 64.45007 65.15124 55.90518 54.04213
[9] 54.03180 65.28280 63.28980 62.74779 61.02095 58.25259 59.66916 54.87424
[17] 59.12766 60.68253 57.41988 61.52291
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.51757 71.42959 71.07248 71.59452 71.78778 69.42486 69.73428 72.48282
[9] 69.16415 NaN
> rowSums(tmp5,na.rm=TRUE)
[1] 1830.351 1428.592 1421.450 1431.890 1435.756 1388.497 1394.686 1449.656
[9] 1383.283 0.000
> rowVars(tmp5,na.rm=TRUE)
[1] 7787.86784 80.12150 79.33344 63.84355 103.14952 87.57861
[7] 38.08450 73.79819 59.69953 NA
> rowSd(tmp5,na.rm=TRUE)
[1] 88.248897 8.951062 8.906932 7.990216 10.156255 9.358344 6.171264
[8] 8.590587 7.726547 NA
> rowMax(tmp5,na.rm=TRUE)
[1] 464.87454 86.98620 87.95879 88.36749 90.82096 92.59649 81.34034
[8] 89.83636 83.23877 NA
> rowMin(tmp5,na.rm=TRUE)
[1] 59.02383 54.87424 58.86037 54.04213 53.86056 56.13214 57.26452 55.90518
[9] 54.93731 NA
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.20879 67.56157 70.51446 71.17862 72.30489 72.18348 72.88042
[8] 70.30111 72.15542 70.60556 75.54166 71.63319 70.18514 71.32450
[15] 75.27284 67.72440 73.96249 67.78019 64.78169 NaN
> colSums(tmp5,na.rm=TRUE)
[1] 1027.8791 608.0541 634.6302 640.6076 650.7440 649.6513 655.9238
[8] 632.7100 649.3988 635.4500 679.8750 644.6987 631.6663 641.9205
[15] 677.4555 609.5196 665.6624 610.0217 583.0352 0.0000
> colVars(tmp5,na.rm=TRUE)
[1] 17385.72353 69.53041 121.08114 127.86007 25.13631 23.88758
[7] 98.48651 120.14219 65.10907 30.86032 53.43189 44.52033
[13] 54.86368 115.42399 95.39108 66.72740 84.66171 61.39461
[19] 47.57350 NA
> colSd(tmp5,na.rm=TRUE)
[1] 131.854934 8.338490 11.003687 11.307523 5.013613 4.887492
[7] 9.924037 10.960939 8.069019 5.555207 7.309712 6.672356
[13] 7.407002 10.743556 9.766836 8.168684 9.201180 7.835471
[19] 6.897355 NA
> colMax(tmp5,na.rm=TRUE)
[1] 464.87454 79.03472 87.95879 89.83636 80.33266 81.29755 85.07278
[8] 85.19666 92.59649 83.23877 83.24003 80.92623 80.60989 90.73350
[15] 88.36749 83.14058 88.15749 85.37682 78.96279 -Inf
> colMin(tmp5,na.rm=TRUE)
[1] 57.26452 57.70167 54.93731 53.86056 64.45007 65.15124 55.90518 54.04213
[9] 66.35044 65.28280 63.54427 62.74779 61.02095 58.25259 59.66916 54.87424
[17] 59.12766 60.68253 57.41988 Inf
>
>
>
>
> 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] 152.20103 176.84434 269.26365 265.80615 275.16985 257.38463 186.45712
[8] 74.63989 220.62774 174.79045
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 152.20103 176.84434 269.26365 265.80615 275.16985 257.38463 186.45712
[8] 74.63989 220.62774 174.79045
>
>
>
> 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] -4.263256e-14 -5.684342e-14 -4.263256e-14 -8.526513e-14 -2.842171e-14
[6] -1.989520e-13 -1.421085e-13 1.421085e-13 0.000000e+00 -2.273737e-13
[11] 1.136868e-13 -1.421085e-14 0.000000e+00 -8.526513e-14 2.273737e-13
[16] 5.684342e-14 1.136868e-13 -2.842171e-14 1.563194e-13 1.136868e-13
>
>
>
>
>
>
>
>
>
>
> ## 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)
+ }
3 14
2 19
9 20
6 14
9 18
9 2
4 6
4 20
6 4
8 16
6 14
7 18
8 16
7 20
2 3
1 18
2 10
9 10
5 8
2 5
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] 2.072164
> Min(tmp)
[1] -2.397648
> mean(tmp)
[1] 0.150836
> Sum(tmp)
[1] 15.0836
> Var(tmp)
[1] 0.868942
>
> rowMeans(tmp)
[1] 0.150836
> rowSums(tmp)
[1] 15.0836
> rowVars(tmp)
[1] 0.868942
> rowSd(tmp)
[1] 0.9321706
> rowMax(tmp)
[1] 2.072164
> rowMin(tmp)
[1] -2.397648
>
> colMeans(tmp)
[1] -2.397648095 1.667341765 0.919177934 1.386824364 0.847463311
[6] 1.092574696 -0.683194135 0.560051961 -1.278053044 -0.531117410
[11] 0.940218177 -0.716760251 1.291290937 0.998442179 -0.096064794
[16] 0.437007911 -0.359192472 -1.501155996 -0.851716678 0.464049607
[21] 1.814686102 0.060698416 -0.387446554 -1.127750929 -0.114869126
[26] 2.045041807 0.575015884 0.561149275 1.181692377 -1.170879275
[31] -0.785022997 -1.162356592 0.190141387 -0.098687549 -0.659861835
[36] 0.106185127 1.425359438 -1.529320385 -1.319513095 -0.368028999
[41] 0.132850111 0.357339248 -0.130437013 0.935965240 1.790752092
[46] 1.443206253 -1.784871618 0.466796853 1.301505866 1.153180826
[51] -0.361633726 1.385226198 0.977582608 -0.259606575 0.200780867
[56] 1.314933816 0.790428423 -1.251780881 -0.700915934 0.007087368
[61] -0.999889085 -0.307196464 1.133935790 0.087114379 -0.439678224
[66] -0.813948193 -0.341621458 0.387053430 0.041071860 0.383222098
[71] 0.967882192 0.756027137 0.169902085 -0.625734056 -0.666581770
[76] 0.899755604 0.826152820 -0.953311172 0.936131515 -0.834554106
[81] -1.191786743 0.392619400 -0.188503164 0.929541285 -0.008723475
[86] -0.761956622 -0.295664080 -0.718874426 -0.026373827 1.158194494
[91] 0.368994425 0.378359813 1.142201524 1.110545376 -0.228579536
[96] 0.400051579 0.955517171 -0.442671449 0.238642853 2.072164079
> colSums(tmp)
[1] -2.397648095 1.667341765 0.919177934 1.386824364 0.847463311
[6] 1.092574696 -0.683194135 0.560051961 -1.278053044 -0.531117410
[11] 0.940218177 -0.716760251 1.291290937 0.998442179 -0.096064794
[16] 0.437007911 -0.359192472 -1.501155996 -0.851716678 0.464049607
[21] 1.814686102 0.060698416 -0.387446554 -1.127750929 -0.114869126
[26] 2.045041807 0.575015884 0.561149275 1.181692377 -1.170879275
[31] -0.785022997 -1.162356592 0.190141387 -0.098687549 -0.659861835
[36] 0.106185127 1.425359438 -1.529320385 -1.319513095 -0.368028999
[41] 0.132850111 0.357339248 -0.130437013 0.935965240 1.790752092
[46] 1.443206253 -1.784871618 0.466796853 1.301505866 1.153180826
[51] -0.361633726 1.385226198 0.977582608 -0.259606575 0.200780867
[56] 1.314933816 0.790428423 -1.251780881 -0.700915934 0.007087368
[61] -0.999889085 -0.307196464 1.133935790 0.087114379 -0.439678224
[66] -0.813948193 -0.341621458 0.387053430 0.041071860 0.383222098
[71] 0.967882192 0.756027137 0.169902085 -0.625734056 -0.666581770
[76] 0.899755604 0.826152820 -0.953311172 0.936131515 -0.834554106
[81] -1.191786743 0.392619400 -0.188503164 0.929541285 -0.008723475
[86] -0.761956622 -0.295664080 -0.718874426 -0.026373827 1.158194494
[91] 0.368994425 0.378359813 1.142201524 1.110545376 -0.228579536
[96] 0.400051579 0.955517171 -0.442671449 0.238642853 2.072164079
> 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] -2.397648095 1.667341765 0.919177934 1.386824364 0.847463311
[6] 1.092574696 -0.683194135 0.560051961 -1.278053044 -0.531117410
[11] 0.940218177 -0.716760251 1.291290937 0.998442179 -0.096064794
[16] 0.437007911 -0.359192472 -1.501155996 -0.851716678 0.464049607
[21] 1.814686102 0.060698416 -0.387446554 -1.127750929 -0.114869126
[26] 2.045041807 0.575015884 0.561149275 1.181692377 -1.170879275
[31] -0.785022997 -1.162356592 0.190141387 -0.098687549 -0.659861835
[36] 0.106185127 1.425359438 -1.529320385 -1.319513095 -0.368028999
[41] 0.132850111 0.357339248 -0.130437013 0.935965240 1.790752092
[46] 1.443206253 -1.784871618 0.466796853 1.301505866 1.153180826
[51] -0.361633726 1.385226198 0.977582608 -0.259606575 0.200780867
[56] 1.314933816 0.790428423 -1.251780881 -0.700915934 0.007087368
[61] -0.999889085 -0.307196464 1.133935790 0.087114379 -0.439678224
[66] -0.813948193 -0.341621458 0.387053430 0.041071860 0.383222098
[71] 0.967882192 0.756027137 0.169902085 -0.625734056 -0.666581770
[76] 0.899755604 0.826152820 -0.953311172 0.936131515 -0.834554106
[81] -1.191786743 0.392619400 -0.188503164 0.929541285 -0.008723475
[86] -0.761956622 -0.295664080 -0.718874426 -0.026373827 1.158194494
[91] 0.368994425 0.378359813 1.142201524 1.110545376 -0.228579536
[96] 0.400051579 0.955517171 -0.442671449 0.238642853 2.072164079
> colMin(tmp)
[1] -2.397648095 1.667341765 0.919177934 1.386824364 0.847463311
[6] 1.092574696 -0.683194135 0.560051961 -1.278053044 -0.531117410
[11] 0.940218177 -0.716760251 1.291290937 0.998442179 -0.096064794
[16] 0.437007911 -0.359192472 -1.501155996 -0.851716678 0.464049607
[21] 1.814686102 0.060698416 -0.387446554 -1.127750929 -0.114869126
[26] 2.045041807 0.575015884 0.561149275 1.181692377 -1.170879275
[31] -0.785022997 -1.162356592 0.190141387 -0.098687549 -0.659861835
[36] 0.106185127 1.425359438 -1.529320385 -1.319513095 -0.368028999
[41] 0.132850111 0.357339248 -0.130437013 0.935965240 1.790752092
[46] 1.443206253 -1.784871618 0.466796853 1.301505866 1.153180826
[51] -0.361633726 1.385226198 0.977582608 -0.259606575 0.200780867
[56] 1.314933816 0.790428423 -1.251780881 -0.700915934 0.007087368
[61] -0.999889085 -0.307196464 1.133935790 0.087114379 -0.439678224
[66] -0.813948193 -0.341621458 0.387053430 0.041071860 0.383222098
[71] 0.967882192 0.756027137 0.169902085 -0.625734056 -0.666581770
[76] 0.899755604 0.826152820 -0.953311172 0.936131515 -0.834554106
[81] -1.191786743 0.392619400 -0.188503164 0.929541285 -0.008723475
[86] -0.761956622 -0.295664080 -0.718874426 -0.026373827 1.158194494
[91] 0.368994425 0.378359813 1.142201524 1.110545376 -0.228579536
[96] 0.400051579 0.955517171 -0.442671449 0.238642853 2.072164079
> colMedians(tmp)
[1] -2.397648095 1.667341765 0.919177934 1.386824364 0.847463311
[6] 1.092574696 -0.683194135 0.560051961 -1.278053044 -0.531117410
[11] 0.940218177 -0.716760251 1.291290937 0.998442179 -0.096064794
[16] 0.437007911 -0.359192472 -1.501155996 -0.851716678 0.464049607
[21] 1.814686102 0.060698416 -0.387446554 -1.127750929 -0.114869126
[26] 2.045041807 0.575015884 0.561149275 1.181692377 -1.170879275
[31] -0.785022997 -1.162356592 0.190141387 -0.098687549 -0.659861835
[36] 0.106185127 1.425359438 -1.529320385 -1.319513095 -0.368028999
[41] 0.132850111 0.357339248 -0.130437013 0.935965240 1.790752092
[46] 1.443206253 -1.784871618 0.466796853 1.301505866 1.153180826
[51] -0.361633726 1.385226198 0.977582608 -0.259606575 0.200780867
[56] 1.314933816 0.790428423 -1.251780881 -0.700915934 0.007087368
[61] -0.999889085 -0.307196464 1.133935790 0.087114379 -0.439678224
[66] -0.813948193 -0.341621458 0.387053430 0.041071860 0.383222098
[71] 0.967882192 0.756027137 0.169902085 -0.625734056 -0.666581770
[76] 0.899755604 0.826152820 -0.953311172 0.936131515 -0.834554106
[81] -1.191786743 0.392619400 -0.188503164 0.929541285 -0.008723475
[86] -0.761956622 -0.295664080 -0.718874426 -0.026373827 1.158194494
[91] 0.368994425 0.378359813 1.142201524 1.110545376 -0.228579536
[96] 0.400051579 0.955517171 -0.442671449 0.238642853 2.072164079
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -2.397648 1.667342 0.9191779 1.386824 0.8474633 1.092575 -0.6831941
[2,] -2.397648 1.667342 0.9191779 1.386824 0.8474633 1.092575 -0.6831941
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.560052 -1.278053 -0.5311174 0.9402182 -0.7167603 1.291291 0.9984422
[2,] 0.560052 -1.278053 -0.5311174 0.9402182 -0.7167603 1.291291 0.9984422
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.09606479 0.4370079 -0.3591925 -1.501156 -0.8517167 0.4640496 1.814686
[2,] -0.09606479 0.4370079 -0.3591925 -1.501156 -0.8517167 0.4640496 1.814686
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.06069842 -0.3874466 -1.127751 -0.1148691 2.045042 0.5750159 0.5611493
[2,] 0.06069842 -0.3874466 -1.127751 -0.1148691 2.045042 0.5750159 0.5611493
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.181692 -1.170879 -0.785023 -1.162357 0.1901414 -0.09868755 -0.6598618
[2,] 1.181692 -1.170879 -0.785023 -1.162357 0.1901414 -0.09868755 -0.6598618
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.1061851 1.425359 -1.52932 -1.319513 -0.368029 0.1328501 0.3573392
[2,] 0.1061851 1.425359 -1.52932 -1.319513 -0.368029 0.1328501 0.3573392
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.130437 0.9359652 1.790752 1.443206 -1.784872 0.4667969 1.301506
[2,] -0.130437 0.9359652 1.790752 1.443206 -1.784872 0.4667969 1.301506
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 1.153181 -0.3616337 1.385226 0.9775826 -0.2596066 0.2007809 1.314934
[2,] 1.153181 -0.3616337 1.385226 0.9775826 -0.2596066 0.2007809 1.314934
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.7904284 -1.251781 -0.7009159 0.007087368 -0.9998891 -0.3071965 1.133936
[2,] 0.7904284 -1.251781 -0.7009159 0.007087368 -0.9998891 -0.3071965 1.133936
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.08711438 -0.4396782 -0.8139482 -0.3416215 0.3870534 0.04107186 0.3832221
[2,] 0.08711438 -0.4396782 -0.8139482 -0.3416215 0.3870534 0.04107186 0.3832221
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.9678822 0.7560271 0.1699021 -0.6257341 -0.6665818 0.8997556 0.8261528
[2,] 0.9678822 0.7560271 0.1699021 -0.6257341 -0.6665818 0.8997556 0.8261528
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.9533112 0.9361315 -0.8345541 -1.191787 0.3926194 -0.1885032 0.9295413
[2,] -0.9533112 0.9361315 -0.8345541 -1.191787 0.3926194 -0.1885032 0.9295413
[,85] [,86] [,87] [,88] [,89] [,90]
[1,] -0.008723475 -0.7619566 -0.2956641 -0.7188744 -0.02637383 1.158194
[2,] -0.008723475 -0.7619566 -0.2956641 -0.7188744 -0.02637383 1.158194
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] 0.3689944 0.3783598 1.142202 1.110545 -0.2285795 0.4000516 0.9555172
[2,] 0.3689944 0.3783598 1.142202 1.110545 -0.2285795 0.4000516 0.9555172
[,98] [,99] [,100]
[1,] -0.4426714 0.2386429 2.072164
[2,] -0.4426714 0.2386429 2.072164
>
>
> Max(tmp2)
[1] 2.608338
> Min(tmp2)
[1] -2.465185
> mean(tmp2)
[1] 0.004122611
> Sum(tmp2)
[1] 0.4122611
> Var(tmp2)
[1] 1.180803
>
> rowMeans(tmp2)
[1] 0.21998249 0.73742004 -0.90742095 2.60833762 -0.74059985 -0.83239462
[7] -0.13791163 -0.63607696 0.46563382 -0.61065697 -1.51036232 1.28522853
[13] -0.47117715 0.25481597 -0.38762867 1.21604159 2.17525186 1.00438766
[19] -0.61234475 0.07149378 -0.05216658 1.52123125 0.40295113 0.74115126
[25] -0.14229666 1.72928337 -0.64293297 1.51906472 -0.29575966 0.02243001
[31] -2.05478938 0.39728109 -0.69209783 0.13601705 -1.11290075 -1.54252633
[37] 1.76818883 0.87590389 2.59264955 -0.80484976 -1.25538797 0.56261529
[43] 0.85108131 -0.33628377 -0.14836520 0.29893787 -2.37490692 0.07908658
[49] -0.22888412 -1.00305607 -0.29459665 -0.42744585 1.31081425 0.33005578
[55] -1.80441559 -0.49569876 1.43259291 -0.42256020 0.44428157 -0.41695405
[61] -0.01450602 -0.60922747 -0.58017634 0.73176874 0.80113079 -2.26067385
[67] 0.58050613 -0.46621033 0.59443970 0.23873940 -0.03396839 -0.10137285
[73] -0.67339194 1.01355233 1.07063270 -0.40691153 0.05253176 -1.52817663
[79] 0.12753932 0.55998102 1.73961303 -1.67623310 1.17720205 -2.46518501
[85] -0.73842471 -1.18529693 1.55085281 0.53648328 1.12235808 2.36581103
[91] 0.65086205 -1.10056746 -0.72499551 -0.53903428 -0.21156294 -1.53673679
[97] -1.77566596 -0.77911277 1.11241364 0.13451194
> rowSums(tmp2)
[1] 0.21998249 0.73742004 -0.90742095 2.60833762 -0.74059985 -0.83239462
[7] -0.13791163 -0.63607696 0.46563382 -0.61065697 -1.51036232 1.28522853
[13] -0.47117715 0.25481597 -0.38762867 1.21604159 2.17525186 1.00438766
[19] -0.61234475 0.07149378 -0.05216658 1.52123125 0.40295113 0.74115126
[25] -0.14229666 1.72928337 -0.64293297 1.51906472 -0.29575966 0.02243001
[31] -2.05478938 0.39728109 -0.69209783 0.13601705 -1.11290075 -1.54252633
[37] 1.76818883 0.87590389 2.59264955 -0.80484976 -1.25538797 0.56261529
[43] 0.85108131 -0.33628377 -0.14836520 0.29893787 -2.37490692 0.07908658
[49] -0.22888412 -1.00305607 -0.29459665 -0.42744585 1.31081425 0.33005578
[55] -1.80441559 -0.49569876 1.43259291 -0.42256020 0.44428157 -0.41695405
[61] -0.01450602 -0.60922747 -0.58017634 0.73176874 0.80113079 -2.26067385
[67] 0.58050613 -0.46621033 0.59443970 0.23873940 -0.03396839 -0.10137285
[73] -0.67339194 1.01355233 1.07063270 -0.40691153 0.05253176 -1.52817663
[79] 0.12753932 0.55998102 1.73961303 -1.67623310 1.17720205 -2.46518501
[85] -0.73842471 -1.18529693 1.55085281 0.53648328 1.12235808 2.36581103
[91] 0.65086205 -1.10056746 -0.72499551 -0.53903428 -0.21156294 -1.53673679
[97] -1.77566596 -0.77911277 1.11241364 0.13451194
> 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] 0.21998249 0.73742004 -0.90742095 2.60833762 -0.74059985 -0.83239462
[7] -0.13791163 -0.63607696 0.46563382 -0.61065697 -1.51036232 1.28522853
[13] -0.47117715 0.25481597 -0.38762867 1.21604159 2.17525186 1.00438766
[19] -0.61234475 0.07149378 -0.05216658 1.52123125 0.40295113 0.74115126
[25] -0.14229666 1.72928337 -0.64293297 1.51906472 -0.29575966 0.02243001
[31] -2.05478938 0.39728109 -0.69209783 0.13601705 -1.11290075 -1.54252633
[37] 1.76818883 0.87590389 2.59264955 -0.80484976 -1.25538797 0.56261529
[43] 0.85108131 -0.33628377 -0.14836520 0.29893787 -2.37490692 0.07908658
[49] -0.22888412 -1.00305607 -0.29459665 -0.42744585 1.31081425 0.33005578
[55] -1.80441559 -0.49569876 1.43259291 -0.42256020 0.44428157 -0.41695405
[61] -0.01450602 -0.60922747 -0.58017634 0.73176874 0.80113079 -2.26067385
[67] 0.58050613 -0.46621033 0.59443970 0.23873940 -0.03396839 -0.10137285
[73] -0.67339194 1.01355233 1.07063270 -0.40691153 0.05253176 -1.52817663
[79] 0.12753932 0.55998102 1.73961303 -1.67623310 1.17720205 -2.46518501
[85] -0.73842471 -1.18529693 1.55085281 0.53648328 1.12235808 2.36581103
[91] 0.65086205 -1.10056746 -0.72499551 -0.53903428 -0.21156294 -1.53673679
[97] -1.77566596 -0.77911277 1.11241364 0.13451194
> rowMin(tmp2)
[1] 0.21998249 0.73742004 -0.90742095 2.60833762 -0.74059985 -0.83239462
[7] -0.13791163 -0.63607696 0.46563382 -0.61065697 -1.51036232 1.28522853
[13] -0.47117715 0.25481597 -0.38762867 1.21604159 2.17525186 1.00438766
[19] -0.61234475 0.07149378 -0.05216658 1.52123125 0.40295113 0.74115126
[25] -0.14229666 1.72928337 -0.64293297 1.51906472 -0.29575966 0.02243001
[31] -2.05478938 0.39728109 -0.69209783 0.13601705 -1.11290075 -1.54252633
[37] 1.76818883 0.87590389 2.59264955 -0.80484976 -1.25538797 0.56261529
[43] 0.85108131 -0.33628377 -0.14836520 0.29893787 -2.37490692 0.07908658
[49] -0.22888412 -1.00305607 -0.29459665 -0.42744585 1.31081425 0.33005578
[55] -1.80441559 -0.49569876 1.43259291 -0.42256020 0.44428157 -0.41695405
[61] -0.01450602 -0.60922747 -0.58017634 0.73176874 0.80113079 -2.26067385
[67] 0.58050613 -0.46621033 0.59443970 0.23873940 -0.03396839 -0.10137285
[73] -0.67339194 1.01355233 1.07063270 -0.40691153 0.05253176 -1.52817663
[79] 0.12753932 0.55998102 1.73961303 -1.67623310 1.17720205 -2.46518501
[85] -0.73842471 -1.18529693 1.55085281 0.53648328 1.12235808 2.36581103
[91] 0.65086205 -1.10056746 -0.72499551 -0.53903428 -0.21156294 -1.53673679
[97] -1.77566596 -0.77911277 1.11241364 0.13451194
>
> colMeans(tmp2)
[1] 0.004122611
> colSums(tmp2)
[1] 0.4122611
> colVars(tmp2)
[1] 1.180803
> colSd(tmp2)
[1] 1.086647
> colMax(tmp2)
[1] 2.608338
> colMin(tmp2)
[1] -2.465185
> colMedians(tmp2)
[1] -0.04306748
> colRanges(tmp2)
[,1]
[1,] -2.465185
[2,] 2.608338
>
> 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] 0.3213227 0.3868357 1.2779092 0.8664308 -3.3491304 -0.6578284
[7] -2.4818866 -2.5994655 0.2522165 -3.8362416
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.0752336
[2,] -0.7634528
[3,] 0.2252054
[4,] 0.5855312
[5,] 1.2128886
>
> rowApply(tmp,sum)
[1] 0.7812284 1.0021252 -0.5546874 -3.5861084 -4.9057705 0.2537449
[7] 1.7355900 -0.1243307 0.1083398 -4.5299689
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 2 4 10 4 5 7 7 9 2
[2,] 10 1 7 6 7 7 10 3 1 8
[3,] 6 10 9 7 9 9 2 5 3 1
[4,] 7 4 10 2 6 1 9 4 10 4
[5,] 5 8 1 3 3 3 8 10 2 9
[6,] 8 3 8 9 1 8 4 8 6 5
[7,] 3 9 5 8 8 6 1 1 4 7
[8,] 2 7 2 4 5 2 3 9 5 10
[9,] 1 5 6 5 10 10 6 2 8 3
[10,] 4 6 3 1 2 4 5 6 7 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.72992272 -2.95117329 -1.53685438 -0.75857989 -2.38457471 1.70700587
[7] 1.01060810 3.54067538 0.95484516 -2.50317100 2.86906203 1.52985403
[13] 0.53840006 0.90882081 0.68852068 -4.11749061 -0.75856089 -1.28436951
[19] -0.01906418 1.08418595
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.79377073
[2,] -0.26091504
[3,] -0.16623963
[4,] 0.06214817
[5,] 1.42885451
>
> rowApply(tmp,sum)
[1] 3.8003969 -2.0741190 1.0633324 -0.6545485 -5.3468448
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 1 10 8 12 20
[2,] 3 5 13 13 2
[3,] 14 1 14 3 17
[4,] 4 17 4 7 18
[5,] 10 11 2 11 3
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -2.79377073 -0.94241593 0.8050599 -0.7922172 0.4802823 0.98873849
[2,] 0.06214817 -0.95800352 -2.4193396 0.7381760 0.1585118 0.56811215
[3,] -0.26091504 0.39646024 0.4987462 -0.7472448 -1.5798364 -0.08219328
[4,] -0.16623963 -0.02889367 -0.8878373 -0.4701676 -0.1835971 0.53543366
[5,] 1.42885451 -1.41832041 0.4665165 0.5128736 -1.2599354 -0.30308514
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.2859889 0.9261259 0.5465613 -0.3792666 1.8821712 0.02366394
[2,] -1.3535273 2.4985667 0.4199767 1.0014964 0.9322958 0.30024047
[3,] 2.1192703 0.5236784 0.3437353 -0.3300575 -1.6398198 -0.32641195
[4,] 1.0547167 -0.2696426 -1.5581736 -1.8093940 2.0271430 1.58413553
[5,] -1.0958406 -0.1380531 1.2027454 -0.9859493 -0.3327282 -0.05177395
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.54820294 -1.2475376 0.98687126 0.3167873 0.5636931 0.97329470
[2,] -0.01186428 0.2260890 -0.03276263 -0.9326379 -0.2983235 -1.51281764
[3,] 0.68726074 0.5961344 0.50314328 -0.9564224 -0.3922052 -0.24628267
[4,] 0.13430028 1.6047017 -0.38953737 -0.8163931 -0.2057923 -0.52248377
[5,] -0.81949962 -0.2705667 -0.37919385 -1.7288246 -0.4259331 0.02391987
[,19] [,20]
[1,] -0.75212219 1.3802858
[2,] 0.28465333 -1.7451094
[3,] -0.17105414 2.1273465
[4,] 0.56346158 -0.8502889
[5,] 0.05599723 0.1719520
>
>
> 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 : 644 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 : 556 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 0.7823243 -0.5999689 -0.522424 0.7687585 0.4699105 -1.440675 -0.4053736
col8 col9 col10 col11 col12 col13 col14
row1 0.1452641 0.1694871 -1.32907 -0.5293588 -0.5442725 1.554908 -1.415303
col15 col16 col17 col18 col19 col20
row1 -0.6970573 2.912119 -0.2264634 -0.4972127 -1.625768 0.08928376
> tmp[,"col10"]
col10
row1 -1.3290699
row2 0.6972587
row3 -1.8526737
row4 -0.3849293
row5 0.6076621
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.7823243 -0.5999689 -0.5224240 0.7687585 0.4699105 -1.4406751 -0.4053736
row5 0.9011763 -1.7985688 -0.5584761 1.5216376 0.5073319 0.1754081 0.5576708
col8 col9 col10 col11 col12 col13 col14
row1 0.1452641 0.1694871 -1.3290699 -0.5293588 -0.5442725 1.554908 -1.4153034
row5 -0.2192473 1.9651388 0.6076621 0.4010803 -0.4350116 -1.717312 -0.4796524
col15 col16 col17 col18 col19 col20
row1 -0.69705733 2.912119 -0.2264634 -0.4972127 -1.625768 0.08928376
row5 -0.07514172 -0.387249 -0.4856856 -0.4733769 1.376502 0.11060705
> tmp[,c("col6","col20")]
col6 col20
row1 -1.4406751 0.08928376
row2 -1.3884844 -1.20896513
row3 -0.9301901 0.90634764
row4 -1.9408121 0.19280479
row5 0.1754081 0.11060705
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.4406751 0.08928376
row5 0.1754081 0.11060705
>
>
>
>
> 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 49.65674 48.61304 48.59018 49.57976 49.4571 104.2064 50.27784 48.70859
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.2052 49.18804 50.89138 51.4345 50.21268 49.4424 50.70548 50.94123
col17 col18 col19 col20
row1 49.77514 50.27813 50.70121 103.8974
> tmp[,"col10"]
col10
row1 49.18804
row2 29.32622
row3 29.37179
row4 29.79223
row5 50.61927
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.65674 48.61304 48.59018 49.57976 49.45710 104.2064 50.27784 48.70859
row5 48.63241 48.94811 49.13537 47.87382 48.93924 105.3279 48.65172 51.91891
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.20520 49.18804 50.89138 51.43450 50.21268 49.44240 50.70548 50.94123
row5 48.92886 50.61927 50.62374 50.70908 49.23275 49.12193 49.03211 49.97642
col17 col18 col19 col20
row1 49.77514 50.27813 50.70121 103.8974
row5 50.16798 49.98131 51.17318 105.0372
> tmp[,c("col6","col20")]
col6 col20
row1 104.20639 103.89740
row2 74.28152 74.39357
row3 73.09265 75.18690
row4 75.22998 76.02326
row5 105.32787 105.03719
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.2064 103.8974
row5 105.3279 105.0372
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.2064 103.8974
row5 105.3279 105.0372
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.1665763
[2,] -0.2620268
[3,] -0.3205177
[4,] -2.4732230
[5,] 0.2409634
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.8298125 1.1836093
[2,] -1.3233083 -3.0594937
[3,] -0.3081236 -0.9262406
[4,] -1.6991001 -0.7673751
[5,] -0.6474762 -0.4817350
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.8699828 -0.17752681
[2,] -1.1565655 -0.03045373
[3,] 1.6586485 -0.47386109
[4,] -0.5032076 1.71294734
[5,] 0.1198893 0.57560378
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.8699828
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.8699828
[2,] -1.1565655
>
>
>
> 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] [,7]
row3 0.9712189 -0.6604757 1.3531361 -0.6821176 -0.5619025 -0.1451744 -0.5456581
row1 0.8946576 0.2554685 0.9881539 1.0994075 2.0488159 0.7811587 -0.1867541
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.1001231 0.2729343 -0.36453084 -0.59190579 0.9630447 -2.023717
row1 -0.9373749 -0.5274288 -0.09303204 -0.07164223 -0.4059884 -1.345186
[,14] [,15] [,16] [,17] [,18] [,19]
row3 0.1723529 -0.3194013 0.3000650 -0.3182349 0.09733915 -0.1298455
row1 1.1832933 0.3662213 -0.1500942 -1.1324365 -1.94466051 -1.6808607
[,20]
row3 1.1064527
row1 0.7377241
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.647457 -0.8734328 0.2654784 0.43817 0.05170153 -1.215628 -0.09366088
[,8] [,9] [,10]
row2 1.476911 1.729918 0.1738449
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.3886869 1.831039 1.068947 2.61893 -1.39765 1.491705 -0.5151875
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.03351159 0.4646096 -0.6929198 -0.7187361 -1.723729 2.029429 -1.288786
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.3548996 1.624585 -0.1469508 -0.5369261 0.4368507 0.2480388
>
>
> 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: 0x600000a64120>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc0225779770"
[2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc024e774d47"
[3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc027a72988f"
[4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc02797e1316"
[5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc02441747aa"
[6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc0254620cd2"
[7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc027137da45"
[8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc029db2215"
[9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc02119a95c1"
[10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc023bddbaee"
[11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc025a1b7df6"
[12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc0242eacfb1"
[13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc0245e98fc9"
[14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc0268def8fa"
[15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMc026ac1ae0"
>
>
> ### 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: 0x600000a00000>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x600000a00000>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x600000a00000>
> rowMedians(tmp)
[1] -0.359840297 0.215111651 -0.068410664 0.396318865 -0.151622502
[6] 0.485952601 0.728178504 -0.198103483 0.370325292 0.363355792
[11] 0.338209396 0.333500742 -0.451028524 -0.055450838 -0.470374452
[16] -0.213848784 -0.020132775 -0.341352595 0.322226857 -0.284369627
[21] -0.145301790 0.216662772 0.129510921 0.392465530 -0.024268810
[26] -0.359091234 -0.533292141 -0.455309763 0.201321523 0.030834977
[31] 0.586529869 0.168179741 -0.831836375 -0.155695126 -0.490153199
[36] -0.172846032 -0.110662914 -0.040047564 0.271526244 0.038721041
[41] -0.307440071 -0.329212739 -0.331800959 -0.122169223 0.202986861
[46] 0.515464663 -0.243562467 0.171751206 0.124583269 0.289347905
[51] 0.101098952 0.191561677 -0.389118888 0.053449984 0.109555839
[56] 0.081917795 -0.532817243 -0.201005782 0.294573804 0.253326465
[61] -0.060991043 -0.135139190 -0.057779249 0.107860557 0.069536465
[66] 0.534589727 0.026110609 0.141792266 0.255072408 -0.016028205
[71] -0.320516026 -0.100364026 0.048878563 0.117717197 -0.043534343
[76] -0.252671248 -0.168900324 -0.189202197 -0.177906475 -0.273341309
[81] -0.578080673 0.518064482 -0.323860673 -0.217399401 0.017829967
[86] -0.181846516 -0.112102887 0.006410850 -0.437652560 -0.554217563
[91] 0.189436900 0.173356443 0.359963905 -0.574452156 -0.150050813
[96] -0.137195482 -0.340690266 0.137458446 -0.041580481 -0.220089706
[101] 0.492623899 0.384561189 0.537075104 -0.311354624 0.028627144
[106] -0.303701259 0.124976214 -0.118966891 0.201614512 0.058597656
[111] 0.207512487 0.315695783 0.504442306 0.007166902 0.157174442
[116] 0.160259103 0.530152210 -0.030604256 -0.714782615 0.011179605
[121] 0.368428358 0.457068796 0.220757700 -0.240458622 0.289637419
[126] -0.875671622 0.042342894 -0.134727796 -0.230875900 -0.384080739
[131] -0.147675401 -0.141085488 -0.335177252 0.285634688 -0.148171946
[136] 0.472719176 0.566088508 -0.249840403 0.477927817 0.300676663
[141] 0.143337891 -0.338964502 -0.092895421 -0.272664406 0.115462708
[146] 0.106003730 -0.496555109 0.270615832 0.306750092 0.401171751
[151] 0.297800443 -0.282187827 -0.059685026 -0.263919211 -0.078679637
[156] -0.362650866 0.183372497 -0.026363774 0.153458289 0.047627220
[161] 0.255371587 0.441748952 0.181331488 -0.504409251 0.474367096
[166] 0.329990488 0.161262405 0.044547338 0.026344685 -0.596933423
[171] 0.251706565 0.126300450 -0.823907246 -0.113350684 -0.259527069
[176] 0.044543972 -0.126298695 0.266882609 0.350490047 -0.307908104
[181] 0.048016102 -0.052783035 -0.199727652 0.098992843 0.191596399
[186] 0.364253071 0.137197522 -0.007618802 -0.443595627 0.223914272
[191] -0.213016711 -0.096778547 -0.032091308 -0.428021705 -0.377865723
[196] 0.194168329 0.637401264 0.105295847 0.169849076 -0.302577099
[201] -0.287586803 -0.185654277 0.235025640 -0.251034070 -0.209787777
[206] -0.517785048 -0.641932005 -0.307766471 -0.211293881 -0.256141185
[211] 0.080700631 0.242432471 -0.091045308 0.118303584 -0.093693312
[216] -0.328816169 0.146252793 0.408571397 0.119209100 -1.068101023
[221] -0.367884001 -0.258315224 -0.089578625 0.224904185 0.331090758
[226] -0.008836332 -0.429832192 0.598264662 0.463678166 -0.570964363
>
> proc.time()
user system elapsed
2.603 14.824 17.889
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
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: 0x600000898000>
> .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: 0x600000898000>
> .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: 0x600000898000>
> .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: 0x600000898000>
> 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: 0x6000008801e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000008801e0>
> .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: 0x6000008801e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000008801e0>
> .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: 0x6000008801e0>
> 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: 0x600000880360>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600000880360>
> .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: 0x600000880360>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600000880360>
> .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: 0x600000880360>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600000880360>
> .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: 0x600000880360>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600000880360>
> .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: 0x600000880360>
> 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: 0x6000008a8000>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x6000008a8000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000008a8000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000008a8000>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1305262bdf90" "BufferedMatrixFile130549da78b9"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1305262bdf90" "BufferedMatrixFile130549da78b9"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000008ec120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000008ec120>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000008ec120>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6000008ec120>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6000008ec120>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6000008ec120>
> .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: 0x6000008a8180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6000008a8180>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6000008a8180>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x6000008a8180>
> 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: 0x6000008f4000>
> .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: 0x6000008f4000>
> rm(P)
>
> proc.time()
user system elapsed
0.325 0.144 0.466
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
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
0.318 0.087 0.419