Ben Bolstad
| Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 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 2025-08-06 13:54 -0400 (Wed, 06 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4813 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
| 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 251/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.73.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | 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: 2025-08-05 19:41:02 -0400 (Tue, 05 Aug 2025) |
| EndedAt: 2025-08-05 19:41:54 -0400 (Tue, 05 Aug 2025) |
| EllapsedTime: 51.8 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_1.73.0.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
0.333 0.147 0.474
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] "Tue Aug 5 19:41:27 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] "Tue Aug 5 19:41:27 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: 0x6000015780c0>
>
>
>
> 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] "Tue Aug 5 19:41:32 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] "Tue Aug 5 19:41:34 2025"
>
> ColMode(tmp2)
<pointer: 0x6000015780c0>
>
>
>
> ### 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,] 99.9144272 2.97370167 0.12993571 0.5928001
[2,] -0.8295515 0.11175507 -0.13964970 -1.1284262
[3,] -0.4388359 -0.03511014 0.04257068 0.3085506
[4,] -0.3508326 1.89575137 0.50317417 0.6290080
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.9144272 2.97370167 0.12993571 0.5928001
[2,] 0.8295515 0.11175507 0.13964970 1.1284262
[3,] 0.4388359 0.03511014 0.04257068 0.3085506
[4,] 0.3508326 1.89575137 0.50317417 0.6290080
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9957204 1.7244424 0.3604660 0.7699351
[2,] 0.9107972 0.3342979 0.3736973 1.0622741
[3,] 0.6624469 0.1873770 0.2063266 0.5554733
[4,] 0.5923112 1.3768629 0.7093477 0.7931002
>
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.87163 45.21813 28.73460 33.29215
[2,] 34.93752 28.45473 28.87662 36.75117
[3,] 32.06331 26.90888 27.10584 30.86328
[4,] 31.27394 40.66438 32.59665 33.56001
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600001528000>
> exp(tmp5)
<pointer: 0x600001528000>
> log(tmp5,2)
<pointer: 0x600001528000>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.0408
> Min(tmp5)
[1] 54.57691
> mean(tmp5)
[1] 72.43032
> Sum(tmp5)
[1] 14486.06
> Var(tmp5)
[1] 872.1176
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.98288 70.18734 67.62636 72.66762 70.14486 74.02493 67.11399 72.43409
[9] 68.08801 71.03311
> rowSums(tmp5)
[1] 1819.658 1403.747 1352.527 1453.352 1402.897 1480.499 1342.280 1448.682
[9] 1361.760 1420.662
> rowVars(tmp5)
[1] 7972.43805 88.53248 72.97334 128.15633 57.74624 56.27405
[7] 65.68719 93.10970 62.70310 84.87391
> rowSd(tmp5)
[1] 89.288510 9.409170 8.542443 11.320615 7.599095 7.501603 8.104764
[8] 9.649337 7.918529 9.212704
> rowMax(tmp5)
[1] 468.04084 89.61651 88.46767 91.47147 83.04589 90.70386 82.81508
[8] 97.45718 88.39077 93.14851
> rowMin(tmp5)
[1] 57.74744 55.43299 56.00731 54.57691 55.72571 60.98382 56.06104 57.08486
[9] 54.87577 55.37180
>
> colMeans(tmp5)
[1] 110.54263 68.65307 67.22928 69.61325 71.11680 73.39730 73.21453
[8] 73.48540 72.35928 70.26195 71.35938 68.64181 68.51919 65.91198
[15] 72.02715 73.10082 70.24903 67.29763 68.62059 73.00530
> colSums(tmp5)
[1] 1105.4263 686.5307 672.2928 696.1325 711.1680 733.9730 732.1453
[8] 734.8540 723.5928 702.6195 713.5938 686.4181 685.1919 659.1198
[15] 720.2715 731.0082 702.4903 672.9763 686.2059 730.0530
> colVars(tmp5)
[1] 15814.92701 143.59599 43.19018 35.56625 68.35014 99.29729
[7] 75.72582 81.53945 64.51033 74.43658 78.39601 58.70082
[13] 82.65044 47.01928 95.97419 60.23262 175.55204 50.29604
[19] 183.70381 137.88760
> colSd(tmp5)
[1] 125.757413 11.983155 6.571923 5.963744 8.267414 9.964803
[7] 8.702059 9.029920 8.031832 8.627664 8.854152 7.661646
[13] 9.091229 6.857061 9.796642 7.760968 13.249605 7.091970
[19] 13.553738 11.742555
> colMax(tmp5)
[1] 468.04084 94.11560 75.52200 77.77541 88.66018 83.80869 84.63130
[8] 87.63845 83.89190 81.94448 85.10274 79.61881 88.39077 75.15374
[15] 93.14851 87.98547 97.45718 81.46651 90.70386 91.47147
> colMin(tmp5)
[1] 64.32375 56.00731 56.41725 58.26277 60.52253 54.87577 57.08486 60.22826
[9] 58.01706 57.74028 61.07388 56.06104 58.19298 55.37180 60.98040 59.58326
[17] 54.57691 57.74744 56.44278 55.72571
>
>
> ### 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] 90.98288 70.18734 67.62636 72.66762 70.14486 74.02493 67.11399 NA
[9] 68.08801 71.03311
> rowSums(tmp5)
[1] 1819.658 1403.747 1352.527 1453.352 1402.897 1480.499 1342.280 NA
[9] 1361.760 1420.662
> rowVars(tmp5)
[1] 7972.43805 88.53248 72.97334 128.15633 57.74624 56.27405
[7] 65.68719 61.66520 62.70310 84.87391
> rowSd(tmp5)
[1] 89.288510 9.409170 8.542443 11.320615 7.599095 7.501603 8.104764
[8] 7.852720 7.918529 9.212704
> rowMax(tmp5)
[1] 468.04084 89.61651 88.46767 91.47147 83.04589 90.70386 82.81508
[8] NA 88.39077 93.14851
> rowMin(tmp5)
[1] 57.74744 55.43299 56.00731 54.57691 55.72571 60.98382 56.06104 NA
[9] 54.87577 55.37180
>
> colMeans(tmp5)
[1] 110.54263 68.65307 67.22928 69.61325 71.11680 73.39730 73.21453
[8] 73.48540 72.35928 70.26195 71.35938 68.64181 68.51919 65.91198
[15] 72.02715 73.10082 NA 67.29763 68.62059 73.00530
> colSums(tmp5)
[1] 1105.4263 686.5307 672.2928 696.1325 711.1680 733.9730 732.1453
[8] 734.8540 723.5928 702.6195 713.5938 686.4181 685.1919 659.1198
[15] 720.2715 731.0082 NA 672.9763 686.2059 730.0530
> colVars(tmp5)
[1] 15814.92701 143.59599 43.19018 35.56625 68.35014 99.29729
[7] 75.72582 81.53945 64.51033 74.43658 78.39601 58.70082
[13] 82.65044 47.01928 95.97419 60.23262 NA 50.29604
[19] 183.70381 137.88760
> colSd(tmp5)
[1] 125.757413 11.983155 6.571923 5.963744 8.267414 9.964803
[7] 8.702059 9.029920 8.031832 8.627664 8.854152 7.661646
[13] 9.091229 6.857061 9.796642 7.760968 NA 7.091970
[19] 13.553738 11.742555
> colMax(tmp5)
[1] 468.04084 94.11560 75.52200 77.77541 88.66018 83.80869 84.63130
[8] 87.63845 83.89190 81.94448 85.10274 79.61881 88.39077 75.15374
[15] 93.14851 87.98547 NA 81.46651 90.70386 91.47147
> colMin(tmp5)
[1] 64.32375 56.00731 56.41725 58.26277 60.52253 54.87577 57.08486 60.22826
[9] 58.01706 57.74028 61.07388 56.06104 58.19298 55.37180 60.98040 59.58326
[17] NA 57.74744 56.44278 55.72571
>
> Max(tmp5,na.rm=TRUE)
[1] 468.0408
> Min(tmp5,na.rm=TRUE)
[1] 54.57691
> mean(tmp5,na.rm=TRUE)
[1] 72.30456
> Sum(tmp5,na.rm=TRUE)
[1] 14388.61
> Var(tmp5,na.rm=TRUE)
[1] 873.3429
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.98288 70.18734 67.62636 72.66762 70.14486 74.02493 67.11399 71.11709
[9] 68.08801 71.03311
> rowSums(tmp5,na.rm=TRUE)
[1] 1819.658 1403.747 1352.527 1453.352 1402.897 1480.499 1342.280 1351.225
[9] 1361.760 1420.662
> rowVars(tmp5,na.rm=TRUE)
[1] 7972.43805 88.53248 72.97334 128.15633 57.74624 56.27405
[7] 65.68719 61.66520 62.70310 84.87391
> rowSd(tmp5,na.rm=TRUE)
[1] 89.288510 9.409170 8.542443 11.320615 7.599095 7.501603 8.104764
[8] 7.852720 7.918529 9.212704
> rowMax(tmp5,na.rm=TRUE)
[1] 468.04084 89.61651 88.46767 91.47147 83.04589 90.70386 82.81508
[8] 83.80869 88.39077 93.14851
> rowMin(tmp5,na.rm=TRUE)
[1] 57.74744 55.43299 56.00731 54.57691 55.72571 60.98382 56.06104 57.08486
[9] 54.87577 55.37180
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.54263 68.65307 67.22928 69.61325 71.11680 73.39730 73.21453
[8] 73.48540 72.35928 70.26195 71.35938 68.64181 68.51919 65.91198
[15] 72.02715 73.10082 67.22590 67.29763 68.62059 73.00530
> colSums(tmp5,na.rm=TRUE)
[1] 1105.4263 686.5307 672.2928 696.1325 711.1680 733.9730 732.1453
[8] 734.8540 723.5928 702.6195 713.5938 686.4181 685.1919 659.1198
[15] 720.2715 731.0082 605.0331 672.9763 686.2059 730.0530
> colVars(tmp5,na.rm=TRUE)
[1] 15814.92701 143.59599 43.19018 35.56625 68.35014 99.29729
[7] 75.72582 81.53945 64.51033 74.43658 78.39601 58.70082
[13] 82.65044 47.01928 95.97419 60.23262 94.67888 50.29604
[19] 183.70381 137.88760
> colSd(tmp5,na.rm=TRUE)
[1] 125.757413 11.983155 6.571923 5.963744 8.267414 9.964803
[7] 8.702059 9.029920 8.031832 8.627664 8.854152 7.661646
[13] 9.091229 6.857061 9.796642 7.760968 9.730307 7.091970
[19] 13.553738 11.742555
> colMax(tmp5,na.rm=TRUE)
[1] 468.04084 94.11560 75.52200 77.77541 88.66018 83.80869 84.63130
[8] 87.63845 83.89190 81.94448 85.10274 79.61881 88.39077 75.15374
[15] 93.14851 87.98547 81.04634 81.46651 90.70386 91.47147
> colMin(tmp5,na.rm=TRUE)
[1] 64.32375 56.00731 56.41725 58.26277 60.52253 54.87577 57.08486 60.22826
[9] 58.01706 57.74028 61.07388 56.06104 58.19298 55.37180 60.98040 59.58326
[17] 54.57691 57.74744 56.44278 55.72571
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.98288 70.18734 67.62636 72.66762 70.14486 74.02493 67.11399 NaN
[9] 68.08801 71.03311
> rowSums(tmp5,na.rm=TRUE)
[1] 1819.658 1403.747 1352.527 1453.352 1402.897 1480.499 1342.280 0.000
[9] 1361.760 1420.662
> rowVars(tmp5,na.rm=TRUE)
[1] 7972.43805 88.53248 72.97334 128.15633 57.74624 56.27405
[7] 65.68719 NA 62.70310 84.87391
> rowSd(tmp5,na.rm=TRUE)
[1] 89.288510 9.409170 8.542443 11.320615 7.599095 7.501603 8.104764
[8] NA 7.918529 9.212704
> rowMax(tmp5,na.rm=TRUE)
[1] 468.04084 89.61651 88.46767 91.47147 83.04589 90.70386 82.81508
[8] NA 88.39077 93.14851
> rowMin(tmp5,na.rm=TRUE)
[1] 57.74744 55.43299 56.00731 54.57691 55.72571 60.98382 56.06104 NA
[9] 54.87577 55.37180
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 115.52376 69.63606 66.30787 69.37256 71.65566 72.24048 75.00672
[8] 74.34798 72.70704 69.25268 70.22550 67.85073 68.85938 64.88512
[15] 72.76753 72.80059 NaN 66.80877 69.26177 71.86188
> colSums(tmp5,na.rm=TRUE)
[1] 1039.7139 626.7245 596.7708 624.3531 644.9010 650.1643 675.0605
[8] 669.1318 654.3633 623.2741 632.0295 610.6565 619.7344 583.9661
[15] 654.9078 655.2053 0.0000 601.2790 623.3559 646.7570
> colVars(tmp5,na.rm=TRUE)
[1] 17512.66165 150.67505 39.03767 39.36031 73.62715 96.65430
[7] 49.05732 83.36136 71.21357 72.28152 73.73149 58.99795
[13] 91.67978 41.03417 101.80409 66.74766 NA 53.89454
[19] 202.04179 140.41542
> colSd(tmp5,na.rm=TRUE)
[1] 132.335413 12.274976 6.248014 6.273780 8.580626 9.831292
[7] 7.004093 9.130244 8.438813 8.501854 8.586704 7.681012
[13] 9.574956 6.405792 10.089801 8.169924 NA 7.341290
[19] 14.214141 11.849701
> colMax(tmp5,na.rm=TRUE)
[1] 468.04084 94.11560 75.49533 77.77541 88.66018 83.04589 84.63130
[8] 87.63845 83.89190 81.94448 85.10274 79.61881 88.39077 73.49789
[15] 93.14851 87.98547 -Inf 81.46651 90.70386 91.47147
> colMin(tmp5,na.rm=TRUE)
[1] 64.32375 56.00731 56.41725 58.26277 60.52253 54.87577 65.03755 60.22826
[9] 58.01706 57.74028 61.07388 56.06104 58.19298 55.37180 60.98040 59.58326
[17] Inf 57.74744 56.44278 55.72571
>
>
>
>
> 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] 248.07830 219.72102 240.52222 271.05609 167.75070 356.16504 75.66499
[8] 210.74685 260.44206 208.21122
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 248.07830 219.72102 240.52222 271.05609 167.75070 356.16504 75.66499
[8] 210.74685 260.44206 208.21122
>
>
>
> 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] 8.526513e-14 0.000000e+00 0.000000e+00 0.000000e+00 -1.421085e-13
[6] 1.705303e-13 1.705303e-13 5.684342e-14 8.526513e-14 2.842171e-14
[11] 2.842171e-14 8.526513e-14 -2.842171e-14 -1.705303e-13 -1.705303e-13
[16] 0.000000e+00 -2.273737e-13 -8.526513e-14 -3.410605e-13 -5.684342e-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)
+ }
8 2
8 15
2 16
2 16
3 2
1 12
9 14
7 19
8 17
2 13
2 13
8 6
2 12
5 7
3 4
7 15
5 9
5 19
5 3
5 7
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] 2.522093
> Min(tmp)
[1] -2.998527
> mean(tmp)
[1] -0.07499009
> Sum(tmp)
[1] -7.499009
> Var(tmp)
[1] 0.8943067
>
> rowMeans(tmp)
[1] -0.07499009
> rowSums(tmp)
[1] -7.499009
> rowVars(tmp)
[1] 0.8943067
> rowSd(tmp)
[1] 0.9456779
> rowMax(tmp)
[1] 2.522093
> rowMin(tmp)
[1] -2.998527
>
> colMeans(tmp)
[1] -1.379165344 0.831930365 -1.373318791 1.569138589 -0.397638100
[6] 0.552090592 0.638576619 0.402428080 -0.216695331 -0.947721052
[11] -0.794004115 0.541496295 0.952858311 -0.355170622 -0.025114636
[16] -0.555915039 -0.032881809 1.631917345 0.269857795 0.278004561
[21] -0.486190923 -0.603948986 -1.479899395 -1.522826627 2.522092932
[26] -1.345557866 1.323712424 0.184621987 2.314817457 1.395957907
[31] -0.232681662 0.274543285 -0.126759116 1.113739718 0.545958926
[36] -0.614497769 0.855605113 -0.846913706 -0.456514892 -0.583707814
[41] -0.753802769 -0.014473769 -0.852562371 -0.629360637 -0.275884928
[46] -0.525825180 0.555680338 0.866122006 -0.126187478 -0.180945157
[51] 0.488635544 -1.403890851 0.189906839 1.562164562 1.270654170
[56] -0.768984741 -0.928209487 -0.136960797 -1.788312674 1.137331808
[61] -0.775926225 0.002650085 -0.756205622 0.948221584 -0.749872900
[66] -0.025377637 0.125582152 -0.778046560 1.157160780 -1.312699396
[71] -1.463679608 -1.227497764 -0.164240314 0.211019932 -0.459452628
[76] 0.239977358 -0.161527512 1.550071574 -0.882164570 0.451986075
[81] -0.397625903 -1.417040502 -0.316666417 -0.855621008 1.329942467
[86] -0.451480821 0.653598880 0.590179881 -0.011278833 0.231692201
[91] -1.092210974 -0.690685604 -0.383595521 -0.288544715 -0.202884344
[96] -0.326561344 0.018692141 1.638563632 -2.998527373 0.033747237
> colSums(tmp)
[1] -1.379165344 0.831930365 -1.373318791 1.569138589 -0.397638100
[6] 0.552090592 0.638576619 0.402428080 -0.216695331 -0.947721052
[11] -0.794004115 0.541496295 0.952858311 -0.355170622 -0.025114636
[16] -0.555915039 -0.032881809 1.631917345 0.269857795 0.278004561
[21] -0.486190923 -0.603948986 -1.479899395 -1.522826627 2.522092932
[26] -1.345557866 1.323712424 0.184621987 2.314817457 1.395957907
[31] -0.232681662 0.274543285 -0.126759116 1.113739718 0.545958926
[36] -0.614497769 0.855605113 -0.846913706 -0.456514892 -0.583707814
[41] -0.753802769 -0.014473769 -0.852562371 -0.629360637 -0.275884928
[46] -0.525825180 0.555680338 0.866122006 -0.126187478 -0.180945157
[51] 0.488635544 -1.403890851 0.189906839 1.562164562 1.270654170
[56] -0.768984741 -0.928209487 -0.136960797 -1.788312674 1.137331808
[61] -0.775926225 0.002650085 -0.756205622 0.948221584 -0.749872900
[66] -0.025377637 0.125582152 -0.778046560 1.157160780 -1.312699396
[71] -1.463679608 -1.227497764 -0.164240314 0.211019932 -0.459452628
[76] 0.239977358 -0.161527512 1.550071574 -0.882164570 0.451986075
[81] -0.397625903 -1.417040502 -0.316666417 -0.855621008 1.329942467
[86] -0.451480821 0.653598880 0.590179881 -0.011278833 0.231692201
[91] -1.092210974 -0.690685604 -0.383595521 -0.288544715 -0.202884344
[96] -0.326561344 0.018692141 1.638563632 -2.998527373 0.033747237
> 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] -1.379165344 0.831930365 -1.373318791 1.569138589 -0.397638100
[6] 0.552090592 0.638576619 0.402428080 -0.216695331 -0.947721052
[11] -0.794004115 0.541496295 0.952858311 -0.355170622 -0.025114636
[16] -0.555915039 -0.032881809 1.631917345 0.269857795 0.278004561
[21] -0.486190923 -0.603948986 -1.479899395 -1.522826627 2.522092932
[26] -1.345557866 1.323712424 0.184621987 2.314817457 1.395957907
[31] -0.232681662 0.274543285 -0.126759116 1.113739718 0.545958926
[36] -0.614497769 0.855605113 -0.846913706 -0.456514892 -0.583707814
[41] -0.753802769 -0.014473769 -0.852562371 -0.629360637 -0.275884928
[46] -0.525825180 0.555680338 0.866122006 -0.126187478 -0.180945157
[51] 0.488635544 -1.403890851 0.189906839 1.562164562 1.270654170
[56] -0.768984741 -0.928209487 -0.136960797 -1.788312674 1.137331808
[61] -0.775926225 0.002650085 -0.756205622 0.948221584 -0.749872900
[66] -0.025377637 0.125582152 -0.778046560 1.157160780 -1.312699396
[71] -1.463679608 -1.227497764 -0.164240314 0.211019932 -0.459452628
[76] 0.239977358 -0.161527512 1.550071574 -0.882164570 0.451986075
[81] -0.397625903 -1.417040502 -0.316666417 -0.855621008 1.329942467
[86] -0.451480821 0.653598880 0.590179881 -0.011278833 0.231692201
[91] -1.092210974 -0.690685604 -0.383595521 -0.288544715 -0.202884344
[96] -0.326561344 0.018692141 1.638563632 -2.998527373 0.033747237
> colMin(tmp)
[1] -1.379165344 0.831930365 -1.373318791 1.569138589 -0.397638100
[6] 0.552090592 0.638576619 0.402428080 -0.216695331 -0.947721052
[11] -0.794004115 0.541496295 0.952858311 -0.355170622 -0.025114636
[16] -0.555915039 -0.032881809 1.631917345 0.269857795 0.278004561
[21] -0.486190923 -0.603948986 -1.479899395 -1.522826627 2.522092932
[26] -1.345557866 1.323712424 0.184621987 2.314817457 1.395957907
[31] -0.232681662 0.274543285 -0.126759116 1.113739718 0.545958926
[36] -0.614497769 0.855605113 -0.846913706 -0.456514892 -0.583707814
[41] -0.753802769 -0.014473769 -0.852562371 -0.629360637 -0.275884928
[46] -0.525825180 0.555680338 0.866122006 -0.126187478 -0.180945157
[51] 0.488635544 -1.403890851 0.189906839 1.562164562 1.270654170
[56] -0.768984741 -0.928209487 -0.136960797 -1.788312674 1.137331808
[61] -0.775926225 0.002650085 -0.756205622 0.948221584 -0.749872900
[66] -0.025377637 0.125582152 -0.778046560 1.157160780 -1.312699396
[71] -1.463679608 -1.227497764 -0.164240314 0.211019932 -0.459452628
[76] 0.239977358 -0.161527512 1.550071574 -0.882164570 0.451986075
[81] -0.397625903 -1.417040502 -0.316666417 -0.855621008 1.329942467
[86] -0.451480821 0.653598880 0.590179881 -0.011278833 0.231692201
[91] -1.092210974 -0.690685604 -0.383595521 -0.288544715 -0.202884344
[96] -0.326561344 0.018692141 1.638563632 -2.998527373 0.033747237
> colMedians(tmp)
[1] -1.379165344 0.831930365 -1.373318791 1.569138589 -0.397638100
[6] 0.552090592 0.638576619 0.402428080 -0.216695331 -0.947721052
[11] -0.794004115 0.541496295 0.952858311 -0.355170622 -0.025114636
[16] -0.555915039 -0.032881809 1.631917345 0.269857795 0.278004561
[21] -0.486190923 -0.603948986 -1.479899395 -1.522826627 2.522092932
[26] -1.345557866 1.323712424 0.184621987 2.314817457 1.395957907
[31] -0.232681662 0.274543285 -0.126759116 1.113739718 0.545958926
[36] -0.614497769 0.855605113 -0.846913706 -0.456514892 -0.583707814
[41] -0.753802769 -0.014473769 -0.852562371 -0.629360637 -0.275884928
[46] -0.525825180 0.555680338 0.866122006 -0.126187478 -0.180945157
[51] 0.488635544 -1.403890851 0.189906839 1.562164562 1.270654170
[56] -0.768984741 -0.928209487 -0.136960797 -1.788312674 1.137331808
[61] -0.775926225 0.002650085 -0.756205622 0.948221584 -0.749872900
[66] -0.025377637 0.125582152 -0.778046560 1.157160780 -1.312699396
[71] -1.463679608 -1.227497764 -0.164240314 0.211019932 -0.459452628
[76] 0.239977358 -0.161527512 1.550071574 -0.882164570 0.451986075
[81] -0.397625903 -1.417040502 -0.316666417 -0.855621008 1.329942467
[86] -0.451480821 0.653598880 0.590179881 -0.011278833 0.231692201
[91] -1.092210974 -0.690685604 -0.383595521 -0.288544715 -0.202884344
[96] -0.326561344 0.018692141 1.638563632 -2.998527373 0.033747237
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.379165 0.8319304 -1.373319 1.569139 -0.3976381 0.5520906 0.6385766
[2,] -1.379165 0.8319304 -1.373319 1.569139 -0.3976381 0.5520906 0.6385766
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.4024281 -0.2166953 -0.9477211 -0.7940041 0.5414963 0.9528583 -0.3551706
[2,] 0.4024281 -0.2166953 -0.9477211 -0.7940041 0.5414963 0.9528583 -0.3551706
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.02511464 -0.555915 -0.03288181 1.631917 0.2698578 0.2780046 -0.4861909
[2,] -0.02511464 -0.555915 -0.03288181 1.631917 0.2698578 0.2780046 -0.4861909
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.603949 -1.479899 -1.522827 2.522093 -1.345558 1.323712 0.184622
[2,] -0.603949 -1.479899 -1.522827 2.522093 -1.345558 1.323712 0.184622
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 2.314817 1.395958 -0.2326817 0.2745433 -0.1267591 1.11374 0.5459589
[2,] 2.314817 1.395958 -0.2326817 0.2745433 -0.1267591 1.11374 0.5459589
[,36] [,37] [,38] [,39] [,40] [,41]
[1,] -0.6144978 0.8556051 -0.8469137 -0.4565149 -0.5837078 -0.7538028
[2,] -0.6144978 0.8556051 -0.8469137 -0.4565149 -0.5837078 -0.7538028
[,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] -0.01447377 -0.8525624 -0.6293606 -0.2758849 -0.5258252 0.5556803 0.866122
[2,] -0.01447377 -0.8525624 -0.6293606 -0.2758849 -0.5258252 0.5556803 0.866122
[,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] -0.1261875 -0.1809452 0.4886355 -1.403891 0.1899068 1.562165 1.270654
[2,] -0.1261875 -0.1809452 0.4886355 -1.403891 0.1899068 1.562165 1.270654
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] -0.7689847 -0.9282095 -0.1369608 -1.788313 1.137332 -0.7759262 0.002650085
[2,] -0.7689847 -0.9282095 -0.1369608 -1.788313 1.137332 -0.7759262 0.002650085
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] -0.7562056 0.9482216 -0.7498729 -0.02537764 0.1255822 -0.7780466 1.157161
[2,] -0.7562056 0.9482216 -0.7498729 -0.02537764 0.1255822 -0.7780466 1.157161
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] -1.312699 -1.46368 -1.227498 -0.1642403 0.2110199 -0.4594526 0.2399774
[2,] -1.312699 -1.46368 -1.227498 -0.1642403 0.2110199 -0.4594526 0.2399774
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] -0.1615275 1.550072 -0.8821646 0.4519861 -0.3976259 -1.417041 -0.3166664
[2,] -0.1615275 1.550072 -0.8821646 0.4519861 -0.3976259 -1.417041 -0.3166664
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] -0.855621 1.329942 -0.4514808 0.6535989 0.5901799 -0.01127883 0.2316922
[2,] -0.855621 1.329942 -0.4514808 0.6535989 0.5901799 -0.01127883 0.2316922
[,91] [,92] [,93] [,94] [,95] [,96]
[1,] -1.092211 -0.6906856 -0.3835955 -0.2885447 -0.2028843 -0.3265613
[2,] -1.092211 -0.6906856 -0.3835955 -0.2885447 -0.2028843 -0.3265613
[,97] [,98] [,99] [,100]
[1,] 0.01869214 1.638564 -2.998527 0.03374724
[2,] 0.01869214 1.638564 -2.998527 0.03374724
>
>
> Max(tmp2)
[1] 2.689872
> Min(tmp2)
[1] -2.127452
> mean(tmp2)
[1] 0.07573553
> Sum(tmp2)
[1] 7.573553
> Var(tmp2)
[1] 0.9141068
>
> rowMeans(tmp2)
[1] 0.43144617 0.07267570 1.94781753 0.50699312 -0.10828706 -0.14138606
[7] 1.00920157 -0.49281731 0.71166607 -0.56801196 -0.37985114 -0.95085608
[13] -0.40588049 -0.88507581 0.87848096 -0.59441396 0.35362779 -1.42548704
[19] 2.68987241 -0.42782886 1.33742409 0.13923033 -0.37379845 -0.85785581
[25] -0.18964107 0.44952457 0.29585072 0.30100583 -1.22659486 0.68883897
[31] 1.32950993 -0.92897446 1.26229081 -1.41460335 0.35883385 -0.34790949
[37] 0.48397615 -1.27635380 -0.75133807 0.81041168 -0.24879045 0.94425896
[43] -0.04840039 0.62029660 0.01481747 -1.29431823 -0.65394365 -0.29208734
[49] 2.06055593 -0.70614923 -1.09112222 0.12048411 0.13010488 0.71421464
[55] 0.45695597 -0.74828232 0.05781745 -0.03183159 0.04692298 -1.43712040
[61] 0.20763999 0.93939151 -0.46854704 -0.13523699 -2.12745249 0.68641749
[67] -0.52623329 0.29325069 -0.89948437 0.47129730 0.01792887 0.36137907
[73] 0.22962232 -1.90594650 1.01252980 1.01620687 1.11980714 -0.04336408
[79] 0.06995942 0.90678925 -1.05411589 0.75099192 2.25779676 0.87144510
[85] -0.79651564 -1.49872009 0.11098040 1.38651383 0.29497651 2.61010243
[91] -0.07489782 -0.62242340 -1.27485979 -1.13171359 1.35213939 1.43560263
[97] 0.70567343 -0.11862236 -0.90155219 1.11870059
> rowSums(tmp2)
[1] 0.43144617 0.07267570 1.94781753 0.50699312 -0.10828706 -0.14138606
[7] 1.00920157 -0.49281731 0.71166607 -0.56801196 -0.37985114 -0.95085608
[13] -0.40588049 -0.88507581 0.87848096 -0.59441396 0.35362779 -1.42548704
[19] 2.68987241 -0.42782886 1.33742409 0.13923033 -0.37379845 -0.85785581
[25] -0.18964107 0.44952457 0.29585072 0.30100583 -1.22659486 0.68883897
[31] 1.32950993 -0.92897446 1.26229081 -1.41460335 0.35883385 -0.34790949
[37] 0.48397615 -1.27635380 -0.75133807 0.81041168 -0.24879045 0.94425896
[43] -0.04840039 0.62029660 0.01481747 -1.29431823 -0.65394365 -0.29208734
[49] 2.06055593 -0.70614923 -1.09112222 0.12048411 0.13010488 0.71421464
[55] 0.45695597 -0.74828232 0.05781745 -0.03183159 0.04692298 -1.43712040
[61] 0.20763999 0.93939151 -0.46854704 -0.13523699 -2.12745249 0.68641749
[67] -0.52623329 0.29325069 -0.89948437 0.47129730 0.01792887 0.36137907
[73] 0.22962232 -1.90594650 1.01252980 1.01620687 1.11980714 -0.04336408
[79] 0.06995942 0.90678925 -1.05411589 0.75099192 2.25779676 0.87144510
[85] -0.79651564 -1.49872009 0.11098040 1.38651383 0.29497651 2.61010243
[91] -0.07489782 -0.62242340 -1.27485979 -1.13171359 1.35213939 1.43560263
[97] 0.70567343 -0.11862236 -0.90155219 1.11870059
> 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] 0.43144617 0.07267570 1.94781753 0.50699312 -0.10828706 -0.14138606
[7] 1.00920157 -0.49281731 0.71166607 -0.56801196 -0.37985114 -0.95085608
[13] -0.40588049 -0.88507581 0.87848096 -0.59441396 0.35362779 -1.42548704
[19] 2.68987241 -0.42782886 1.33742409 0.13923033 -0.37379845 -0.85785581
[25] -0.18964107 0.44952457 0.29585072 0.30100583 -1.22659486 0.68883897
[31] 1.32950993 -0.92897446 1.26229081 -1.41460335 0.35883385 -0.34790949
[37] 0.48397615 -1.27635380 -0.75133807 0.81041168 -0.24879045 0.94425896
[43] -0.04840039 0.62029660 0.01481747 -1.29431823 -0.65394365 -0.29208734
[49] 2.06055593 -0.70614923 -1.09112222 0.12048411 0.13010488 0.71421464
[55] 0.45695597 -0.74828232 0.05781745 -0.03183159 0.04692298 -1.43712040
[61] 0.20763999 0.93939151 -0.46854704 -0.13523699 -2.12745249 0.68641749
[67] -0.52623329 0.29325069 -0.89948437 0.47129730 0.01792887 0.36137907
[73] 0.22962232 -1.90594650 1.01252980 1.01620687 1.11980714 -0.04336408
[79] 0.06995942 0.90678925 -1.05411589 0.75099192 2.25779676 0.87144510
[85] -0.79651564 -1.49872009 0.11098040 1.38651383 0.29497651 2.61010243
[91] -0.07489782 -0.62242340 -1.27485979 -1.13171359 1.35213939 1.43560263
[97] 0.70567343 -0.11862236 -0.90155219 1.11870059
> rowMin(tmp2)
[1] 0.43144617 0.07267570 1.94781753 0.50699312 -0.10828706 -0.14138606
[7] 1.00920157 -0.49281731 0.71166607 -0.56801196 -0.37985114 -0.95085608
[13] -0.40588049 -0.88507581 0.87848096 -0.59441396 0.35362779 -1.42548704
[19] 2.68987241 -0.42782886 1.33742409 0.13923033 -0.37379845 -0.85785581
[25] -0.18964107 0.44952457 0.29585072 0.30100583 -1.22659486 0.68883897
[31] 1.32950993 -0.92897446 1.26229081 -1.41460335 0.35883385 -0.34790949
[37] 0.48397615 -1.27635380 -0.75133807 0.81041168 -0.24879045 0.94425896
[43] -0.04840039 0.62029660 0.01481747 -1.29431823 -0.65394365 -0.29208734
[49] 2.06055593 -0.70614923 -1.09112222 0.12048411 0.13010488 0.71421464
[55] 0.45695597 -0.74828232 0.05781745 -0.03183159 0.04692298 -1.43712040
[61] 0.20763999 0.93939151 -0.46854704 -0.13523699 -2.12745249 0.68641749
[67] -0.52623329 0.29325069 -0.89948437 0.47129730 0.01792887 0.36137907
[73] 0.22962232 -1.90594650 1.01252980 1.01620687 1.11980714 -0.04336408
[79] 0.06995942 0.90678925 -1.05411589 0.75099192 2.25779676 0.87144510
[85] -0.79651564 -1.49872009 0.11098040 1.38651383 0.29497651 2.61010243
[91] -0.07489782 -0.62242340 -1.27485979 -1.13171359 1.35213939 1.43560263
[97] 0.70567343 -0.11862236 -0.90155219 1.11870059
>
> colMeans(tmp2)
[1] 0.07573553
> colSums(tmp2)
[1] 7.573553
> colVars(tmp2)
[1] 0.9141068
> colSd(tmp2)
[1] 0.9560893
> colMax(tmp2)
[1] 2.689872
> colMin(tmp2)
[1] -2.127452
> colMedians(tmp2)
[1] 0.06388844
> colRanges(tmp2)
[,1]
[1,] -2.127452
[2,] 2.689872
>
> 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] 0.01735534 0.06585036 2.99445137 -4.03738446 1.39188612 -3.09990568
[7] -4.12968678 -3.81906654 -0.06501803 0.93059467
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.4872224
[2,] -0.4072328
[3,] 0.3183746
[4,] 0.5133523
[5,] 0.9580157
>
> rowApply(tmp,sum)
[1] -8.3895677 2.2376640 0.1765017 -3.6538508 0.9203668 -1.2063333
[7] 0.5941830 -1.0956596 2.4865270 -1.8207546
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 10 7 6 10 3 1 8 10 2 6
[2,] 4 6 8 7 2 2 7 1 7 10
[3,] 1 8 10 8 10 4 9 5 3 9
[4,] 2 3 1 3 9 5 10 4 6 1
[5,] 9 2 2 5 4 10 6 7 10 8
[6,] 7 4 4 2 7 7 5 8 1 4
[7,] 6 5 3 1 6 6 3 6 4 7
[8,] 8 1 5 9 8 3 4 2 5 3
[9,] 3 10 7 4 1 9 1 9 9 5
[10,] 5 9 9 6 5 8 2 3 8 2
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.5823769 -2.3740524 1.6715648 2.5216934 2.7671637 1.4830332
[7] 1.2455641 -2.1684888 -5.5157608 0.8987463 -0.5631230 -1.2401053
[13] 2.8116616 -3.7939037 -0.2195383 2.2074426 -1.0545123 -0.7306974
[19] 1.4888191 2.4890148
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.3435550
[2,] 0.8237207
[3,] 0.8524749
[4,] 1.1095269
[5,] 1.1402095
>
> rowApply(tmp,sum)
[1] 1.71174974 0.06363364 3.24564869 0.69777165 -0.21190519
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 16 6 16 16 17
[2,] 4 17 6 2 11
[3,] 17 20 15 3 7
[4,] 18 19 17 10 3
[5,] 9 13 18 19 10
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.8524749 -0.68688820 0.9140877 1.30286677 -0.20483956 1.3122559
[2,] -0.3435550 0.73702178 1.7969725 1.51354528 0.04173067 -0.2018026
[3,] 1.1402095 -0.44042743 0.8981309 1.21072501 1.23769819 1.4398592
[4,] 0.8237207 -1.91324064 -1.6697907 0.08174265 1.81501025 -0.3724949
[5,] 1.1095269 -0.07051792 -0.2678356 -1.58718634 -0.12243585 -0.6947844
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.6226567 -0.37455549 0.3054922 -0.04952635 -1.9784822 -0.2393451
[2,] -1.3543518 0.17963530 -0.2901167 -0.01530868 -0.6250058 -0.5141265
[3,] 0.1080494 -0.96596282 -1.1616369 0.30109959 -0.9475464 0.7885060
[4,] 1.1340721 -0.09933259 -1.9887925 0.60213446 2.7310735 -1.3668740
[5,] 1.9804511 -0.90827316 -2.3807070 0.06034733 0.2568380 0.0917343
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.12917301 -0.42984116 0.4859449 0.6031052 -0.1283487 -0.7764710
[2,] 1.00653565 -1.96158509 -0.2548868 0.2081099 0.6132349 -0.3624900
[3,] 1.44344254 0.34676250 -0.8686890 0.1463908 -1.9738127 0.4035699
[4,] 0.08432368 -0.06631654 0.6742442 -0.4857270 0.5656936 0.2871123
[5,] 1.40653278 -1.68292342 -0.2561515 1.7355637 -0.1312793 -0.2824186
[,19] [,20]
[1,] 2.07086127 0.484788532
[2,] 0.02735857 -0.137282018
[3,] 0.13913166 0.000148744
[4,] -1.27698614 1.138199195
[5,] 0.52845373 1.003160347
>
>
> 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 : 653 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 : 565 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 0.8415723 -0.4991497 0.2528496 0.8057274 0.2570561 1.06783 -0.2410271
col8 col9 col10 col11 col12 col13 col14
row1 0.04240166 -1.058744 2.016265 1.611267 1.352358 1.129347 -1.080392
col15 col16 col17 col18 col19 col20
row1 2.340832 1.304275 -1.020169 0.3933088 -1.908232 -0.9678327
> tmp[,"col10"]
col10
row1 2.01626542
row2 -0.72205940
row3 -0.05474211
row4 0.39491726
row5 -0.66622798
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.8415723 -0.49914971 0.2528496 0.8057274 0.2570561 1.067830 -0.2410271
row5 0.4370302 -0.08112031 -0.5712818 0.4382687 -0.5571600 1.203201 -0.9904122
col8 col9 col10 col11 col12 col13 col14
row1 0.04240166 -1.0587443 2.016265 1.6112671 1.352358 1.1293466 -1.080392
row5 -0.18424276 0.1161626 -0.666228 -0.3905292 -2.003549 0.9232708 1.643304
col15 col16 col17 col18 col19 col20
row1 2.340832 1.3042749 -1.020169 0.3933088 -1.908232 -0.9678327
row5 1.031638 0.3586446 1.483515 -0.4742870 -0.656236 1.2857559
> tmp[,c("col6","col20")]
col6 col20
row1 1.0678302 -0.9678327
row2 -1.4658940 -2.1229002
row3 0.2068473 0.1938951
row4 0.3877930 -0.5982847
row5 1.2032014 1.2857559
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 1.067830 -0.9678327
row5 1.203201 1.2857559
>
>
>
>
> 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 47.41181 50.9067 50.98749 47.66885 49.32254 103.8021 49.62884 50.07822
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.47312 48.20737 50.30735 52.15305 49.25204 50.37502 51.53209 50.2783
col17 col18 col19 col20
row1 50.15387 50.89773 50.10975 103.7906
> tmp[,"col10"]
col10
row1 48.20737
row2 29.84891
row3 30.17374
row4 29.99514
row5 50.03097
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 47.41181 50.90670 50.98749 47.66885 49.32254 103.8021 49.62884 50.07822
row5 49.59234 48.95565 47.02644 49.36440 50.30248 105.4475 50.34207 48.31339
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.47312 48.20737 50.30735 52.15305 49.25204 50.37502 51.53209 50.27830
row5 50.01845 50.03097 51.17655 48.41604 49.42068 51.20238 49.88210 51.29539
col17 col18 col19 col20
row1 50.15387 50.89773 50.10975 103.7906
row5 49.56681 49.83847 51.01797 103.3863
> tmp[,c("col6","col20")]
col6 col20
row1 103.80206 103.79062
row2 75.68449 74.07266
row3 75.08375 74.12960
row4 75.36143 74.74249
row5 105.44747 103.38629
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.8021 103.7906
row5 105.4475 103.3863
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.8021 103.7906
row5 105.4475 103.3863
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.66028480
[2,] -1.03437272
[3,] 0.04960473
[4,] -0.32143391
[5,] -0.63482167
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.302985405 -1.67999284
[2,] 1.750846127 0.08119830
[3,] 1.320458789 -1.02282508
[4,] -0.008184181 0.12076766
[5,] 1.076464745 -0.08268343
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 1.7937962 -0.79715659
[2,] 0.6292411 0.07236893
[3,] 0.7199981 -0.30459330
[4,] -2.2340847 1.05420165
[5,] 1.0577709 -0.20321452
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 1.793796
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 1.7937962
[2,] 0.6292411
>
>
>
> 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 0.816304 -2.801957 1.69213 1.6395543 0.888347451 -1.9024898 -0.3726371
row1 1.222034 0.459533 1.09097 -0.6982408 0.009067748 -0.5225836 1.8881993
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.5141696 -1.4023694 -0.5929874 2.4097173 -0.7425844 -0.0170325
row1 1.4953292 -0.9234606 -0.1722807 -0.6323433 0.4151549 1.3831724
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 0.1569336 -0.007413777 1.004979 -0.1910161 0.48428189 1.453281 0.9232217
row1 0.7034837 -1.182769530 -0.478716 -0.4216599 0.07492065 1.543196 1.1173221
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.7428975 1.126671 -0.05062042 1.208912 2.81157 0.5129749 0.05862669
[,8] [,9] [,10]
row2 1.616663 0.6154174 -0.4640197
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.4719692 -0.1114195 1.205147 0.4003967 1.195784 -0.1633122 0.9196893
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.8300942 0.9097538 1.464136 0.7954834 1.016654 0.9481907 -0.2004323
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.06779259 1.049439 0.2201955 -0.4500866 -0.09675158 0.2693978
>
>
> 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: 0x60000152c000>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd446fe96d7"
[2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd4746121aa"
[3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd414e95b97"
[4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd4647c213a"
[5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd411699a60"
[6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd42c161d8e"
[7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd45fee6c3e"
[8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd41e048ba6"
[9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd43c6c4eaf"
[10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd46aa1e226"
[11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd42a06637b"
[12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd496d35cb"
[13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd460e6a742"
[14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd446ef0fc1"
[15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM10fd478f36c48"
>
>
> ### 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: 0x6000015fc000>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6000015fc000>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6000015fc000>
> rowMedians(tmp)
[1] -0.783328326 -0.477297650 0.573160715 -0.200964996 -0.140262481
[6] 0.022801753 0.191955397 -0.032218161 -0.022245085 -0.170889067
[11] -0.649606131 0.001017300 0.259964986 -0.079114404 0.051072323
[16] -0.008626351 -0.237172766 -0.127693843 -0.144470532 0.240912208
[21] -0.169155049 -0.294486661 -0.012145514 0.097016398 -0.010290934
[26] -0.037221475 -0.114481986 -0.034345607 -1.094185041 -0.007356902
[31] -0.447963966 0.367826665 -0.114897860 0.091591829 -0.327449429
[36] -0.096724435 -0.618157741 0.278142986 -0.504219258 -0.240207502
[41] -0.092763762 -0.138025899 0.260537638 -0.314423295 0.115705872
[46] 0.169751079 -0.079691507 -0.065427586 -0.039525423 -0.414359295
[51] -0.013317238 0.125312887 0.349154790 -0.104952205 0.096891574
[56] 0.421119876 -0.097776047 0.579240383 -0.342858243 -0.029869755
[61] 0.024888288 -0.084508813 0.265871017 0.309124597 0.220504748
[66] -0.252836048 0.162602893 0.255289209 -0.424072941 0.024337627
[71] 0.073794366 0.379466896 0.108452511 0.018145359 -0.007602386
[76] -0.035967101 -0.063448534 -0.216580827 0.091826736 0.633813442
[81] 0.072645357 -0.040966665 -0.107058975 0.349984057 -0.190291228
[86] -0.340390256 -0.221188300 0.037791246 0.015600857 -0.198348567
[91] 0.313739122 0.197484070 -0.175965521 -0.539454571 0.563744385
[96] 0.298274676 -0.118868445 0.205160671 0.007290186 0.167685122
[101] 0.731426528 0.199711673 0.235196685 -0.484009727 0.114972875
[106] -0.358725726 -0.143901817 0.048243045 -0.114324401 0.087438068
[111] -0.129925211 -0.483110986 -0.315754553 -0.155969510 0.155203795
[116] 0.085682334 0.031268121 -0.204345345 0.086392586 0.006924686
[121] 0.376727791 0.388033011 0.146383486 0.018066040 -0.481272200
[126] 0.314323068 -0.036308142 -0.445637794 0.395224774 0.062544349
[131] -0.010035794 0.008850213 0.164004326 -0.100150133 -0.519574185
[136] 0.061113330 0.404100820 -0.125514584 -0.192523697 -0.438411972
[141] 0.070609503 0.503805185 0.352258497 0.125435669 0.138722995
[146] -0.018873795 -0.212321054 0.116714479 -0.194895982 0.453778126
[151] 0.125644879 0.227754807 0.102215188 -0.136563155 0.331330027
[156] -0.046656787 -0.206739787 0.153625762 -0.277855034 0.183762491
[161] 0.094575750 0.345367918 -0.185670592 0.332008673 0.153450793
[166] 0.389560717 0.306978135 0.319350168 -0.115575194 -0.331378343
[171] 0.014676760 -0.358770099 0.331187609 -0.578043127 0.637228150
[176] -0.160663783 -0.304992328 0.365937351 0.077052119 -0.408575650
[181] -0.324158927 0.521695250 -0.083392161 -0.109400973 -0.101221949
[186] -0.605400031 -0.459566061 0.054118166 -0.619395031 -0.160699620
[191] -0.036149254 0.233927744 -0.104228363 -0.172138570 0.584349795
[196] 0.068710362 -0.160236606 -0.301790390 0.307626558 -0.129390037
[201] -0.003785800 -0.165173717 -0.251034291 0.023175169 0.640082382
[206] 0.054087560 0.427130744 -0.052635923 0.308588319 -0.384168818
[211] -0.085382428 -0.355114494 1.059769555 0.650167133 0.002987807
[216] 0.402901194 0.060528720 0.119267698 0.450527290 -0.279135437
[221] 0.383956034 0.596435869 -0.165755323 -0.184651716 -0.073118507
[226] -0.384952963 -0.050928114 0.201784006 0.040989347 0.437794813
>
> proc.time()
user system elapsed
2.661 15.317 18.669
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: 0x600002f30000>
> .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: 0x600002f30000>
> .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: 0x600002f30000>
> .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: 0x600002f30000>
> 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: 0x600002f40000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002f40000>
> .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: 0x600002f40000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002f40000>
> .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: 0x600002f40000>
> 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: 0x600002f40180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002f40180>
> .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: 0x600002f40180>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600002f40180>
> .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: 0x600002f40180>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600002f40180>
> .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: 0x600002f40180>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600002f40180>
> .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: 0x600002f40180>
> 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: 0x600002f40360>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600002f40360>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002f40360>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002f40360>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile115b010d7738c" "BufferedMatrixFile115b0606b0028"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile115b010d7738c" "BufferedMatrixFile115b0606b0028"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002f44120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002f44120>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600002f44120>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600002f44120>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600002f44120>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600002f44120>
> .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: 0x600002f58000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600002f58000>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600002f58000>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x600002f58000>
> 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: 0x600002f58180>
> .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: 0x600002f58180>
> rm(P)
>
> proc.time()
user system elapsed
0.327 0.145 0.467
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
0.340 0.099 0.416