Ben Bolstad
| Snapshot Date: 2025-05-09 13:00 -0400 (Fri, 09 May 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 2025-05-11 12:08 -0400 (Sun, 11 May 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4749 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4510 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4489 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4449 |
| 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 250/2304 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.73.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.1 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 | | ||||||||
| 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: 2025-05-09 19:35:25 -0400 (Fri, 09 May 2025) |
| EndedAt: 2025-05-09 19:36:19 -0400 (Fri, 09 May 2025) |
| EllapsedTime: 53.9 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 4.5.0 Patched (2025-04-21 r88169)
* 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 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
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
0.345 0.148 0.483
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
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 480829 25.7 1056567 56.5 NA 634460 33.9
Vcells 891038 6.8 8388608 64.0 98304 2108473 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 May 9 19:35:49 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 May 9 19:35:49 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: 0x600000388000>
>
>
>
> 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 May 9 19:35:55 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 May 9 19:35:56 2025"
>
> ColMode(tmp2)
<pointer: 0x600000388000>
>
>
>
> ### 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,] 99.1847028 1.8179621 -0.3067778 -1.3966477
[2,] 0.6101502 1.5575332 -2.0934298 -0.4091534
[3,] 0.3143060 0.4192273 -0.7799008 0.5627296
[4,] -0.3133959 0.1362084 0.7134991 -1.5542486
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.1847028 1.8179621 0.3067778 1.3966477
[2,] 0.6101502 1.5575332 2.0934298 0.4091534
[3,] 0.3143060 0.4192273 0.7799008 0.5627296
[4,] 0.3133959 0.1362084 0.7134991 1.5542486
> 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,] 9.9591517 1.3483183 0.5538752 1.181798
[2,] 0.7811211 1.2480117 1.4468690 0.639651
[3,] 0.5606300 0.6474776 0.8831199 0.750153
[4,] 0.5598178 0.3690642 0.8446887 1.246695
>
> 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,] 223.77622 40.30114 30.84553 38.21463
[2,] 33.42136 39.03765 41.56212 31.80566
[3,] 30.92061 31.89400 34.61110 33.06426
[4,] 30.91157 28.82685 34.16039 39.02120
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600000380000>
> exp(tmp5)
<pointer: 0x600000380000>
> log(tmp5,2)
<pointer: 0x600000380000>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 465.7609
> Min(tmp5)
[1] 52.98831
> mean(tmp5)
[1] 72.21238
> Sum(tmp5)
[1] 14442.48
> Var(tmp5)
[1] 853.3907
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.62526 69.59397 68.35810 68.78413 71.38078 71.19291 71.24356 68.75921
[9] 69.58497 72.60093
> rowSums(tmp5)
[1] 1812.505 1391.879 1367.162 1375.683 1427.616 1423.858 1424.871 1375.184
[9] 1391.699 1452.019
> rowVars(tmp5)
[1] 7903.97807 80.03057 82.23331 47.39912 77.00936 43.60067
[7] 92.50323 67.90810 58.77848 69.81248
> rowSd(tmp5)
[1] 88.904320 8.945981 9.068258 6.884702 8.775498 6.603080 9.617860
[8] 8.240637 7.666713 8.355386
> rowMax(tmp5)
[1] 465.76088 86.50611 84.47228 81.21751 86.35244 84.45650 88.62461
[8] 80.61088 87.97754 87.91841
> rowMin(tmp5)
[1] 57.66006 57.05839 54.83906 55.26416 56.43210 62.77270 52.98831 53.43391
[9] 59.87372 56.43802
>
> colMeans(tmp5)
[1] 112.57020 69.21048 72.45570 71.06959 71.84081 69.76668 67.13756
[8] 69.00759 67.37860 70.92563 73.18063 67.25626 71.17337 72.74826
[15] 71.17528 68.89077 65.48706 68.71591 71.42183 72.83541
> colSums(tmp5)
[1] 1125.7020 692.1048 724.5570 710.6959 718.4081 697.6668 671.3756
[8] 690.0759 673.7860 709.2563 731.8063 672.5626 711.7337 727.4826
[15] 711.7528 688.9077 654.8706 687.1591 714.2183 728.3541
> colVars(tmp5)
[1] 15466.48516 83.76609 89.74419 82.28039 41.27036 66.34501
[7] 104.98270 51.87233 98.09136 51.44430 139.24371 70.45936
[13] 76.27180 111.77774 58.95957 35.68959 65.56454 47.21484
[19] 46.94536 76.85249
> colSd(tmp5)
[1] 124.364324 9.152382 9.473341 9.070854 6.424201 8.145245
[7] 10.246107 7.202245 9.904108 7.172468 11.800157 8.394007
[13] 8.733373 10.572499 7.678513 5.974076 8.097193 6.871305
[19] 6.851669 8.766555
> colMax(tmp5)
[1] 465.76088 83.88155 87.91841 83.85792 80.47722 84.49593 80.34488
[8] 81.50561 86.35244 81.07470 94.26008 83.26016 87.97754 85.26996
[15] 84.47228 78.21414 78.11757 78.51800 84.12654 84.52386
> colMin(tmp5)
[1] 64.33839 56.43210 61.10383 57.02772 64.17009 59.24793 52.98831 58.79255
[9] 55.26416 59.16993 53.43391 54.83906 56.43802 57.10618 59.92205 60.67404
[17] 56.74500 57.71377 62.32973 62.74608
>
>
> ### 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] 90.62526 69.59397 68.35810 68.78413 71.38078 71.19291 NA 68.75921
[9] 69.58497 72.60093
> rowSums(tmp5)
[1] 1812.505 1391.879 1367.162 1375.683 1427.616 1423.858 NA 1375.184
[9] 1391.699 1452.019
> rowVars(tmp5)
[1] 7903.97807 80.03057 82.23331 47.39912 77.00936 43.60067
[7] 94.96059 67.90810 58.77848 69.81248
> rowSd(tmp5)
[1] 88.904320 8.945981 9.068258 6.884702 8.775498 6.603080 9.744772
[8] 8.240637 7.666713 8.355386
> rowMax(tmp5)
[1] 465.76088 86.50611 84.47228 81.21751 86.35244 84.45650 NA
[8] 80.61088 87.97754 87.91841
> rowMin(tmp5)
[1] 57.66006 57.05839 54.83906 55.26416 56.43210 62.77270 NA 53.43391
[9] 59.87372 56.43802
>
> colMeans(tmp5)
[1] 112.57020 69.21048 72.45570 71.06959 NA 69.76668 67.13756
[8] 69.00759 67.37860 70.92563 73.18063 67.25626 71.17337 72.74826
[15] 71.17528 68.89077 65.48706 68.71591 71.42183 72.83541
> colSums(tmp5)
[1] 1125.7020 692.1048 724.5570 710.6959 NA 697.6668 671.3756
[8] 690.0759 673.7860 709.2563 731.8063 672.5626 711.7337 727.4826
[15] 711.7528 688.9077 654.8706 687.1591 714.2183 728.3541
> colVars(tmp5)
[1] 15466.48516 83.76609 89.74419 82.28039 NA 66.34501
[7] 104.98270 51.87233 98.09136 51.44430 139.24371 70.45936
[13] 76.27180 111.77774 58.95957 35.68959 65.56454 47.21484
[19] 46.94536 76.85249
> colSd(tmp5)
[1] 124.364324 9.152382 9.473341 9.070854 NA 8.145245
[7] 10.246107 7.202245 9.904108 7.172468 11.800157 8.394007
[13] 8.733373 10.572499 7.678513 5.974076 8.097193 6.871305
[19] 6.851669 8.766555
> colMax(tmp5)
[1] 465.76088 83.88155 87.91841 83.85792 NA 84.49593 80.34488
[8] 81.50561 86.35244 81.07470 94.26008 83.26016 87.97754 85.26996
[15] 84.47228 78.21414 78.11757 78.51800 84.12654 84.52386
> colMin(tmp5)
[1] 64.33839 56.43210 61.10383 57.02772 NA 59.24793 52.98831 58.79255
[9] 55.26416 59.16993 53.43391 54.83906 56.43802 57.10618 59.92205 60.67404
[17] 56.74500 57.71377 62.32973 62.74608
>
> Max(tmp5,na.rm=TRUE)
[1] 465.7609
> Min(tmp5,na.rm=TRUE)
[1] 52.98831
> mean(tmp5,na.rm=TRUE)
[1] 72.25128
> Sum(tmp5,na.rm=TRUE)
[1] 14378
> Var(tmp5,na.rm=TRUE)
[1] 857.3966
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.62526 69.59397 68.35810 68.78413 71.38078 71.19291 71.59997 68.75921
[9] 69.58497 72.60093
> rowSums(tmp5,na.rm=TRUE)
[1] 1812.505 1391.879 1367.162 1375.683 1427.616 1423.858 1360.399 1375.184
[9] 1391.699 1452.019
> rowVars(tmp5,na.rm=TRUE)
[1] 7903.97807 80.03057 82.23331 47.39912 77.00936 43.60067
[7] 94.96059 67.90810 58.77848 69.81248
> rowSd(tmp5,na.rm=TRUE)
[1] 88.904320 8.945981 9.068258 6.884702 8.775498 6.603080 9.744772
[8] 8.240637 7.666713 8.355386
> rowMax(tmp5,na.rm=TRUE)
[1] 465.76088 86.50611 84.47228 81.21751 86.35244 84.45650 88.62461
[8] 80.61088 87.97754 87.91841
> rowMin(tmp5,na.rm=TRUE)
[1] 57.66006 57.05839 54.83906 55.26416 56.43210 62.77270 52.98831 53.43391
[9] 59.87372 56.43802
>
> colMeans(tmp5,na.rm=TRUE)
[1] 112.57020 69.21048 72.45570 71.06959 72.65959 69.76668 67.13756
[8] 69.00759 67.37860 70.92563 73.18063 67.25626 71.17337 72.74826
[15] 71.17528 68.89077 65.48706 68.71591 71.42183 72.83541
> colSums(tmp5,na.rm=TRUE)
[1] 1125.7020 692.1048 724.5570 710.6959 653.9363 697.6668 671.3756
[8] 690.0759 673.7860 709.2563 731.8063 672.5626 711.7337 727.4826
[15] 711.7528 688.9077 654.8706 687.1591 714.2183 728.3541
> colVars(tmp5,na.rm=TRUE)
[1] 15466.48516 83.76609 89.74419 82.28039 38.88707 66.34501
[7] 104.98270 51.87233 98.09136 51.44430 139.24371 70.45936
[13] 76.27180 111.77774 58.95957 35.68959 65.56454 47.21484
[19] 46.94536 76.85249
> colSd(tmp5,na.rm=TRUE)
[1] 124.364324 9.152382 9.473341 9.070854 6.235950 8.145245
[7] 10.246107 7.202245 9.904108 7.172468 11.800157 8.394007
[13] 8.733373 10.572499 7.678513 5.974076 8.097193 6.871305
[19] 6.851669 8.766555
> colMax(tmp5,na.rm=TRUE)
[1] 465.76088 83.88155 87.91841 83.85792 80.47722 84.49593 80.34488
[8] 81.50561 86.35244 81.07470 94.26008 83.26016 87.97754 85.26996
[15] 84.47228 78.21414 78.11757 78.51800 84.12654 84.52386
> colMin(tmp5,na.rm=TRUE)
[1] 64.33839 56.43210 61.10383 57.02772 64.17009 59.24793 52.98831 58.79255
[9] 55.26416 59.16993 53.43391 54.83906 56.43802 57.10618 59.92205 60.67404
[17] 56.74500 57.71377 62.32973 62.74608
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.62526 69.59397 68.35810 68.78413 71.38078 71.19291 NaN 68.75921
[9] 69.58497 72.60093
> rowSums(tmp5,na.rm=TRUE)
[1] 1812.505 1391.879 1367.162 1375.683 1427.616 1423.858 0.000 1375.184
[9] 1391.699 1452.019
> rowVars(tmp5,na.rm=TRUE)
[1] 7903.97807 80.03057 82.23331 47.39912 77.00936 43.60067
[7] NA 67.90810 58.77848 69.81248
> rowSd(tmp5,na.rm=TRUE)
[1] 88.904320 8.945981 9.068258 6.884702 8.775498 6.603080 NA
[8] 8.240637 7.666713 8.355386
> rowMax(tmp5,na.rm=TRUE)
[1] 465.76088 86.50611 84.47228 81.21751 86.35244 84.45650 NA
[8] 80.61088 87.97754 87.91841
> rowMin(tmp5,na.rm=TRUE)
[1] 57.66006 57.05839 54.83906 55.26416 56.43210 62.77270 NA 53.43391
[9] 59.87372 56.43802
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 115.23082 69.05156 71.49733 69.64866 NaN 70.50301 68.70970
[8] 69.16152 67.16898 69.80465 71.54200 67.37523 71.44434 73.20015
[15] 70.31225 68.94679 66.35090 68.75300 71.16563 73.87444
> colSums(tmp5,na.rm=TRUE)
[1] 1037.0774 621.4641 643.4760 626.8379 0.0000 634.5270 618.3873
[8] 622.4537 604.5208 628.2418 643.8780 606.3771 642.9991 658.8013
[15] 632.8103 620.5211 597.1581 618.7770 640.4907 664.8700
> colVars(tmp5,na.rm=TRUE)
[1] 17320.15811 93.95273 90.62943 69.85135 NA 68.53876
[7] 90.29978 58.08980 109.85846 43.73806 126.44179 79.10755
[13] 84.97971 123.45269 57.95033 40.11548 65.36507 53.10122
[19] 52.07511 74.31360
> colSd(tmp5,na.rm=TRUE)
[1] 131.606072 9.692922 9.519949 8.357712 NA 8.278814
[7] 9.502620 7.621667 10.481339 6.613476 11.244634 8.894242
[13] 9.218444 11.110927 7.612511 6.333679 8.084867 7.287058
[19] 7.216308 8.620534
> colMax(tmp5,na.rm=TRUE)
[1] 465.76088 83.88155 87.91841 81.21751 -Inf 84.49593 80.34488
[8] 81.50561 86.35244 81.07470 94.26008 83.26016 87.97754 85.26996
[15] 84.47228 78.21414 78.11757 78.51800 84.12654 84.52386
> colMin(tmp5,na.rm=TRUE)
[1] 64.33839 56.43210 61.10383 57.02772 Inf 59.24793 57.42810 58.79255
[9] 55.26416 59.16993 53.43391 54.83906 56.43802 57.10618 59.92205 60.67404
[17] 56.74500 57.71377 62.32973 62.74608
>
>
>
>
> 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] 269.4156 202.7350 122.8836 442.4624 214.3697 183.6696 144.3623 186.5742
[9] 187.8155 312.8606
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 269.4156 202.7350 122.8836 442.4624 214.3697 183.6696 144.3623 186.5742
[9] 187.8155 312.8606
>
>
>
> 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] -5.684342e-14 2.842171e-14 -8.526513e-14 0.000000e+00 8.526513e-14
[6] -1.705303e-13 -2.842171e-14 -5.684342e-14 1.136868e-13 5.684342e-14
[11] -1.136868e-13 -2.557954e-13 1.705303e-13 -3.410605e-13 4.263256e-14
[16] 1.136868e-13 1.350031e-13 -5.684342e-14 -5.684342e-14 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## 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 4
7 7
7 8
1 20
6 1
8 6
6 8
2 12
2 8
10 17
2 18
8 13
5 1
9 3
7 16
8 19
3 6
5 8
2 7
5 11
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] 2.467654
> Min(tmp)
[1] -2.492655
> mean(tmp)
[1] 0.1059891
> Sum(tmp)
[1] 10.59891
> Var(tmp)
[1] 1.066065
>
> rowMeans(tmp)
[1] 0.1059891
> rowSums(tmp)
[1] 10.59891
> rowVars(tmp)
[1] 1.066065
> rowSd(tmp)
[1] 1.032504
> rowMax(tmp)
[1] 2.467654
> rowMin(tmp)
[1] -2.492655
>
> colMeans(tmp)
[1] -2.105347987 2.467654032 -1.525412379 1.834640832 0.504930750
[6] 0.061220353 1.862757502 -0.670427957 1.417345786 0.184965766
[11] -0.435436880 0.062630533 -0.334500250 -1.612549560 -1.948524128
[16] 0.682696655 0.993069371 -0.223196535 0.870340845 1.353579794
[21] -0.530113970 0.638016478 0.147776184 -0.358687730 1.280125458
[26] -2.223397170 0.416588918 0.148041925 1.225619357 -0.722195578
[31] 1.910289757 -0.764501834 1.708752129 0.678072303 -0.440431414
[36] 0.407982100 -1.380281608 0.572156129 1.798503644 0.746052511
[41] -1.253666507 -1.074146143 -0.706263079 -0.144413419 0.669393043
[46] -0.351222404 0.505082458 -0.436889128 -0.014995133 -0.507152938
[51] 0.832524227 0.718278379 -1.146400176 -0.246995613 0.340337715
[56] 0.430342473 -0.245979531 1.106033786 1.267913358 0.361336987
[61] -0.157683993 -1.598995956 -0.743607490 0.720447837 0.151670393
[66] 0.690927487 -0.008530247 0.108998924 -0.296875566 -0.410775039
[71] 1.219511527 0.410525716 0.851720883 1.468316924 -0.784484467
[76] 1.012098723 0.720696827 1.991157235 -0.455448938 1.308299823
[81] 0.781376014 -0.774969710 0.662277597 -1.596008459 0.341200916
[86] 0.264019882 -1.532398633 -2.492655279 0.237230831 0.165270170
[91] -0.881073642 0.575463186 0.663559505 -1.654096184 1.012190921
[96] -1.381092417 0.675646862 -0.217890359 1.192886952 -0.441924998
> colSums(tmp)
[1] -2.105347987 2.467654032 -1.525412379 1.834640832 0.504930750
[6] 0.061220353 1.862757502 -0.670427957 1.417345786 0.184965766
[11] -0.435436880 0.062630533 -0.334500250 -1.612549560 -1.948524128
[16] 0.682696655 0.993069371 -0.223196535 0.870340845 1.353579794
[21] -0.530113970 0.638016478 0.147776184 -0.358687730 1.280125458
[26] -2.223397170 0.416588918 0.148041925 1.225619357 -0.722195578
[31] 1.910289757 -0.764501834 1.708752129 0.678072303 -0.440431414
[36] 0.407982100 -1.380281608 0.572156129 1.798503644 0.746052511
[41] -1.253666507 -1.074146143 -0.706263079 -0.144413419 0.669393043
[46] -0.351222404 0.505082458 -0.436889128 -0.014995133 -0.507152938
[51] 0.832524227 0.718278379 -1.146400176 -0.246995613 0.340337715
[56] 0.430342473 -0.245979531 1.106033786 1.267913358 0.361336987
[61] -0.157683993 -1.598995956 -0.743607490 0.720447837 0.151670393
[66] 0.690927487 -0.008530247 0.108998924 -0.296875566 -0.410775039
[71] 1.219511527 0.410525716 0.851720883 1.468316924 -0.784484467
[76] 1.012098723 0.720696827 1.991157235 -0.455448938 1.308299823
[81] 0.781376014 -0.774969710 0.662277597 -1.596008459 0.341200916
[86] 0.264019882 -1.532398633 -2.492655279 0.237230831 0.165270170
[91] -0.881073642 0.575463186 0.663559505 -1.654096184 1.012190921
[96] -1.381092417 0.675646862 -0.217890359 1.192886952 -0.441924998
> 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] -2.105347987 2.467654032 -1.525412379 1.834640832 0.504930750
[6] 0.061220353 1.862757502 -0.670427957 1.417345786 0.184965766
[11] -0.435436880 0.062630533 -0.334500250 -1.612549560 -1.948524128
[16] 0.682696655 0.993069371 -0.223196535 0.870340845 1.353579794
[21] -0.530113970 0.638016478 0.147776184 -0.358687730 1.280125458
[26] -2.223397170 0.416588918 0.148041925 1.225619357 -0.722195578
[31] 1.910289757 -0.764501834 1.708752129 0.678072303 -0.440431414
[36] 0.407982100 -1.380281608 0.572156129 1.798503644 0.746052511
[41] -1.253666507 -1.074146143 -0.706263079 -0.144413419 0.669393043
[46] -0.351222404 0.505082458 -0.436889128 -0.014995133 -0.507152938
[51] 0.832524227 0.718278379 -1.146400176 -0.246995613 0.340337715
[56] 0.430342473 -0.245979531 1.106033786 1.267913358 0.361336987
[61] -0.157683993 -1.598995956 -0.743607490 0.720447837 0.151670393
[66] 0.690927487 -0.008530247 0.108998924 -0.296875566 -0.410775039
[71] 1.219511527 0.410525716 0.851720883 1.468316924 -0.784484467
[76] 1.012098723 0.720696827 1.991157235 -0.455448938 1.308299823
[81] 0.781376014 -0.774969710 0.662277597 -1.596008459 0.341200916
[86] 0.264019882 -1.532398633 -2.492655279 0.237230831 0.165270170
[91] -0.881073642 0.575463186 0.663559505 -1.654096184 1.012190921
[96] -1.381092417 0.675646862 -0.217890359 1.192886952 -0.441924998
> colMin(tmp)
[1] -2.105347987 2.467654032 -1.525412379 1.834640832 0.504930750
[6] 0.061220353 1.862757502 -0.670427957 1.417345786 0.184965766
[11] -0.435436880 0.062630533 -0.334500250 -1.612549560 -1.948524128
[16] 0.682696655 0.993069371 -0.223196535 0.870340845 1.353579794
[21] -0.530113970 0.638016478 0.147776184 -0.358687730 1.280125458
[26] -2.223397170 0.416588918 0.148041925 1.225619357 -0.722195578
[31] 1.910289757 -0.764501834 1.708752129 0.678072303 -0.440431414
[36] 0.407982100 -1.380281608 0.572156129 1.798503644 0.746052511
[41] -1.253666507 -1.074146143 -0.706263079 -0.144413419 0.669393043
[46] -0.351222404 0.505082458 -0.436889128 -0.014995133 -0.507152938
[51] 0.832524227 0.718278379 -1.146400176 -0.246995613 0.340337715
[56] 0.430342473 -0.245979531 1.106033786 1.267913358 0.361336987
[61] -0.157683993 -1.598995956 -0.743607490 0.720447837 0.151670393
[66] 0.690927487 -0.008530247 0.108998924 -0.296875566 -0.410775039
[71] 1.219511527 0.410525716 0.851720883 1.468316924 -0.784484467
[76] 1.012098723 0.720696827 1.991157235 -0.455448938 1.308299823
[81] 0.781376014 -0.774969710 0.662277597 -1.596008459 0.341200916
[86] 0.264019882 -1.532398633 -2.492655279 0.237230831 0.165270170
[91] -0.881073642 0.575463186 0.663559505 -1.654096184 1.012190921
[96] -1.381092417 0.675646862 -0.217890359 1.192886952 -0.441924998
> colMedians(tmp)
[1] -2.105347987 2.467654032 -1.525412379 1.834640832 0.504930750
[6] 0.061220353 1.862757502 -0.670427957 1.417345786 0.184965766
[11] -0.435436880 0.062630533 -0.334500250 -1.612549560 -1.948524128
[16] 0.682696655 0.993069371 -0.223196535 0.870340845 1.353579794
[21] -0.530113970 0.638016478 0.147776184 -0.358687730 1.280125458
[26] -2.223397170 0.416588918 0.148041925 1.225619357 -0.722195578
[31] 1.910289757 -0.764501834 1.708752129 0.678072303 -0.440431414
[36] 0.407982100 -1.380281608 0.572156129 1.798503644 0.746052511
[41] -1.253666507 -1.074146143 -0.706263079 -0.144413419 0.669393043
[46] -0.351222404 0.505082458 -0.436889128 -0.014995133 -0.507152938
[51] 0.832524227 0.718278379 -1.146400176 -0.246995613 0.340337715
[56] 0.430342473 -0.245979531 1.106033786 1.267913358 0.361336987
[61] -0.157683993 -1.598995956 -0.743607490 0.720447837 0.151670393
[66] 0.690927487 -0.008530247 0.108998924 -0.296875566 -0.410775039
[71] 1.219511527 0.410525716 0.851720883 1.468316924 -0.784484467
[76] 1.012098723 0.720696827 1.991157235 -0.455448938 1.308299823
[81] 0.781376014 -0.774969710 0.662277597 -1.596008459 0.341200916
[86] 0.264019882 -1.532398633 -2.492655279 0.237230831 0.165270170
[91] -0.881073642 0.575463186 0.663559505 -1.654096184 1.012190921
[96] -1.381092417 0.675646862 -0.217890359 1.192886952 -0.441924998
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -2.105348 2.467654 -1.525412 1.834641 0.5049307 0.06122035 1.862758
[2,] -2.105348 2.467654 -1.525412 1.834641 0.5049307 0.06122035 1.862758
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.670428 1.417346 0.1849658 -0.4354369 0.06263053 -0.3345003 -1.61255
[2,] -0.670428 1.417346 0.1849658 -0.4354369 0.06263053 -0.3345003 -1.61255
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.948524 0.6826967 0.9930694 -0.2231965 0.8703408 1.35358 -0.530114
[2,] -1.948524 0.6826967 0.9930694 -0.2231965 0.8703408 1.35358 -0.530114
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.6380165 0.1477762 -0.3586877 1.280125 -2.223397 0.4165889 0.1480419
[2,] 0.6380165 0.1477762 -0.3586877 1.280125 -2.223397 0.4165889 0.1480419
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.225619 -0.7221956 1.91029 -0.7645018 1.708752 0.6780723 -0.4404314
[2,] 1.225619 -0.7221956 1.91029 -0.7645018 1.708752 0.6780723 -0.4404314
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.4079821 -1.380282 0.5721561 1.798504 0.7460525 -1.253667 -1.074146
[2,] 0.4079821 -1.380282 0.5721561 1.798504 0.7460525 -1.253667 -1.074146
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.7062631 -0.1444134 0.669393 -0.3512224 0.5050825 -0.4368891 -0.01499513
[2,] -0.7062631 -0.1444134 0.669393 -0.3512224 0.5050825 -0.4368891 -0.01499513
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.5071529 0.8325242 0.7182784 -1.1464 -0.2469956 0.3403377 0.4303425
[2,] -0.5071529 0.8325242 0.7182784 -1.1464 -0.2469956 0.3403377 0.4303425
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.2459795 1.106034 1.267913 0.361337 -0.157684 -1.598996 -0.7436075
[2,] -0.2459795 1.106034 1.267913 0.361337 -0.157684 -1.598996 -0.7436075
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.7204478 0.1516704 0.6909275 -0.008530247 0.1089989 -0.2968756 -0.410775
[2,] 0.7204478 0.1516704 0.6909275 -0.008530247 0.1089989 -0.2968756 -0.410775
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 1.219512 0.4105257 0.8517209 1.468317 -0.7844845 1.012099 0.7206968
[2,] 1.219512 0.4105257 0.8517209 1.468317 -0.7844845 1.012099 0.7206968
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 1.991157 -0.4554489 1.3083 0.781376 -0.7749697 0.6622776 -1.596008
[2,] 1.991157 -0.4554489 1.3083 0.781376 -0.7749697 0.6622776 -1.596008
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.3412009 0.2640199 -1.532399 -2.492655 0.2372308 0.1652702 -0.8810736
[2,] 0.3412009 0.2640199 -1.532399 -2.492655 0.2372308 0.1652702 -0.8810736
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.5754632 0.6635595 -1.654096 1.012191 -1.381092 0.6756469 -0.2178904
[2,] 0.5754632 0.6635595 -1.654096 1.012191 -1.381092 0.6756469 -0.2178904
[,99] [,100]
[1,] 1.192887 -0.441925
[2,] 1.192887 -0.441925
>
>
> Max(tmp2)
[1] 2.107378
> Min(tmp2)
[1] -2.899293
> mean(tmp2)
[1] 0.06318066
> Sum(tmp2)
[1] 6.318066
> Var(tmp2)
[1] 1.009293
>
> rowMeans(tmp2)
[1] -0.48345767 -0.06278484 0.68472276 -1.21484094 1.12233241 0.80203888
[7] 2.04841533 1.75230196 -0.79074738 0.03411291 -0.91294389 0.84479905
[13] 1.32343759 0.82061615 1.04029046 0.33743196 -0.98926784 -0.87726746
[19] 0.88290865 -1.12182475 0.93357858 0.88283468 0.05479805 -0.87359464
[25] -0.17114066 -1.59627313 -1.49767617 1.54507312 -0.02502106 0.88333947
[31] -1.45706155 -1.55326264 0.78193128 -0.28270880 0.99725507 2.10737767
[37] -0.23357593 -0.34640195 -0.17707108 -2.68765889 0.95807060 0.67388270
[43] -1.42156217 0.63058109 0.68571719 1.11287508 -0.10252621 -1.80518283
[49] -0.70662251 0.88534478 -1.02095549 0.13417710 -0.49624391 -0.32042917
[55] 0.60584460 1.57277916 0.45540442 -2.89929303 0.29217819 -0.69941842
[61] -0.15316917 0.38905821 -0.56340216 0.09380145 -0.11066376 1.46833255
[67] -0.53765087 -0.44139999 -0.01817215 -0.13770603 -1.17216391 -0.35244722
[73] -0.48313048 0.49337802 -0.13835915 0.26756762 -0.16893714 -0.39703924
[79] 1.33022489 -0.45644863 -2.14649276 1.55301368 1.08951888 1.61975791
[85] -0.09334299 -0.76369686 1.02800814 1.18437011 0.71688871 0.22930418
[91] -0.68899861 0.65147679 -0.24020468 1.32342148 -0.03010288 -0.03485305
[97] -1.07321012 0.62575398 1.09864368 0.29750190
> rowSums(tmp2)
[1] -0.48345767 -0.06278484 0.68472276 -1.21484094 1.12233241 0.80203888
[7] 2.04841533 1.75230196 -0.79074738 0.03411291 -0.91294389 0.84479905
[13] 1.32343759 0.82061615 1.04029046 0.33743196 -0.98926784 -0.87726746
[19] 0.88290865 -1.12182475 0.93357858 0.88283468 0.05479805 -0.87359464
[25] -0.17114066 -1.59627313 -1.49767617 1.54507312 -0.02502106 0.88333947
[31] -1.45706155 -1.55326264 0.78193128 -0.28270880 0.99725507 2.10737767
[37] -0.23357593 -0.34640195 -0.17707108 -2.68765889 0.95807060 0.67388270
[43] -1.42156217 0.63058109 0.68571719 1.11287508 -0.10252621 -1.80518283
[49] -0.70662251 0.88534478 -1.02095549 0.13417710 -0.49624391 -0.32042917
[55] 0.60584460 1.57277916 0.45540442 -2.89929303 0.29217819 -0.69941842
[61] -0.15316917 0.38905821 -0.56340216 0.09380145 -0.11066376 1.46833255
[67] -0.53765087 -0.44139999 -0.01817215 -0.13770603 -1.17216391 -0.35244722
[73] -0.48313048 0.49337802 -0.13835915 0.26756762 -0.16893714 -0.39703924
[79] 1.33022489 -0.45644863 -2.14649276 1.55301368 1.08951888 1.61975791
[85] -0.09334299 -0.76369686 1.02800814 1.18437011 0.71688871 0.22930418
[91] -0.68899861 0.65147679 -0.24020468 1.32342148 -0.03010288 -0.03485305
[97] -1.07321012 0.62575398 1.09864368 0.29750190
> 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] -0.48345767 -0.06278484 0.68472276 -1.21484094 1.12233241 0.80203888
[7] 2.04841533 1.75230196 -0.79074738 0.03411291 -0.91294389 0.84479905
[13] 1.32343759 0.82061615 1.04029046 0.33743196 -0.98926784 -0.87726746
[19] 0.88290865 -1.12182475 0.93357858 0.88283468 0.05479805 -0.87359464
[25] -0.17114066 -1.59627313 -1.49767617 1.54507312 -0.02502106 0.88333947
[31] -1.45706155 -1.55326264 0.78193128 -0.28270880 0.99725507 2.10737767
[37] -0.23357593 -0.34640195 -0.17707108 -2.68765889 0.95807060 0.67388270
[43] -1.42156217 0.63058109 0.68571719 1.11287508 -0.10252621 -1.80518283
[49] -0.70662251 0.88534478 -1.02095549 0.13417710 -0.49624391 -0.32042917
[55] 0.60584460 1.57277916 0.45540442 -2.89929303 0.29217819 -0.69941842
[61] -0.15316917 0.38905821 -0.56340216 0.09380145 -0.11066376 1.46833255
[67] -0.53765087 -0.44139999 -0.01817215 -0.13770603 -1.17216391 -0.35244722
[73] -0.48313048 0.49337802 -0.13835915 0.26756762 -0.16893714 -0.39703924
[79] 1.33022489 -0.45644863 -2.14649276 1.55301368 1.08951888 1.61975791
[85] -0.09334299 -0.76369686 1.02800814 1.18437011 0.71688871 0.22930418
[91] -0.68899861 0.65147679 -0.24020468 1.32342148 -0.03010288 -0.03485305
[97] -1.07321012 0.62575398 1.09864368 0.29750190
> rowMin(tmp2)
[1] -0.48345767 -0.06278484 0.68472276 -1.21484094 1.12233241 0.80203888
[7] 2.04841533 1.75230196 -0.79074738 0.03411291 -0.91294389 0.84479905
[13] 1.32343759 0.82061615 1.04029046 0.33743196 -0.98926784 -0.87726746
[19] 0.88290865 -1.12182475 0.93357858 0.88283468 0.05479805 -0.87359464
[25] -0.17114066 -1.59627313 -1.49767617 1.54507312 -0.02502106 0.88333947
[31] -1.45706155 -1.55326264 0.78193128 -0.28270880 0.99725507 2.10737767
[37] -0.23357593 -0.34640195 -0.17707108 -2.68765889 0.95807060 0.67388270
[43] -1.42156217 0.63058109 0.68571719 1.11287508 -0.10252621 -1.80518283
[49] -0.70662251 0.88534478 -1.02095549 0.13417710 -0.49624391 -0.32042917
[55] 0.60584460 1.57277916 0.45540442 -2.89929303 0.29217819 -0.69941842
[61] -0.15316917 0.38905821 -0.56340216 0.09380145 -0.11066376 1.46833255
[67] -0.53765087 -0.44139999 -0.01817215 -0.13770603 -1.17216391 -0.35244722
[73] -0.48313048 0.49337802 -0.13835915 0.26756762 -0.16893714 -0.39703924
[79] 1.33022489 -0.45644863 -2.14649276 1.55301368 1.08951888 1.61975791
[85] -0.09334299 -0.76369686 1.02800814 1.18437011 0.71688871 0.22930418
[91] -0.68899861 0.65147679 -0.24020468 1.32342148 -0.03010288 -0.03485305
[97] -1.07321012 0.62575398 1.09864368 0.29750190
>
> colMeans(tmp2)
[1] 0.06318066
> colSums(tmp2)
[1] 6.318066
> colVars(tmp2)
[1] 1.009293
> colSd(tmp2)
[1] 1.004636
> colMax(tmp2)
[1] 2.107378
> colMin(tmp2)
[1] -2.899293
> colMedians(tmp2)
[1] -0.0215966
> colRanges(tmp2)
[,1]
[1,] -2.899293
[2,] 2.107378
>
> 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] -1.10131957 1.67888823 -0.02711363 4.53882669 -4.98173416 3.28774862
[7] 3.91333141 -2.07189571 -2.91629463 -3.36852360
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.3734255
[2,] -0.6572419
[3,] -0.1176988
[4,] 0.4608879
[5,] 0.9346363
>
> rowApply(tmp,sum)
[1] 0.6656368 4.6644237 0.6430398 -2.4682819 2.9156327 -2.9227775
[7] -3.2189706 -3.2826139 4.2637564 -2.3079317
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 7 5 2 3 8 9 4 6 2
[2,] 6 4 2 4 10 7 4 8 3 8
[3,] 1 3 9 5 8 10 3 10 2 1
[4,] 7 6 1 10 9 3 5 9 9 10
[5,] 5 9 3 1 4 1 6 3 1 7
[6,] 8 10 8 6 2 5 1 7 10 9
[7,] 10 2 6 8 6 9 8 6 8 5
[8,] 2 1 10 9 5 4 2 1 7 6
[9,] 3 5 7 7 7 6 7 2 4 3
[10,] 4 8 4 3 1 2 10 5 5 4
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.2874096 5.3314783 0.9697682 -0.4332665 3.2071149 2.9596486
[7] -1.2202419 1.9572458 0.2011688 0.4428000 -2.0563960 0.3077874
[13] -1.1516821 1.5047610 0.2210919 -2.3836302 0.1393196 0.3522167
[19] 1.0320830 0.6439584
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.1794771
[2,] -0.9697557
[3,] -0.5032184
[4,] 0.4815224
[5,] 0.8835193
>
> rowApply(tmp,sum)
[1] 1.6539659 6.0980477 0.3886696 -4.9551518 7.5522851
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 18 3 2 8 12
[2,] 14 16 18 15 20
[3,] 4 19 10 9 16
[4,] 2 15 12 11 9
[5,] 15 18 17 14 10
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.8835193 0.5242881 -1.10424181 -1.2798914 0.5498428 1.9523831
[2,] -0.9697557 1.1143799 1.54265319 0.8107516 1.2326401 -0.4616839
[3,] -1.1794771 0.9898389 -0.03541552 0.1967418 0.7111181 0.2998662
[4,] -0.5032184 0.4331604 -0.46682104 -0.4125983 0.4244767 0.5416832
[5,] 0.4815224 2.2698111 1.03359340 0.2517298 0.2890372 0.6274000
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.2646482 -0.3917545 1.46272229 0.8306986 -0.7473414 0.4395303
[2,] 0.6230872 1.1512247 -1.09288439 -0.3453769 -1.4056673 0.1489540
[3,] 1.0606630 0.3538387 0.27679871 -0.6706259 0.3703865 -1.4899300
[4,] -1.6063351 -1.0148110 -0.41929730 -0.8374904 -1.0464044 1.5160257
[5,] -1.5623053 1.8587480 -0.02617049 1.4655946 0.7726306 -0.3067926
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.47427117 -0.2626634 -0.02123224 -1.3111632 0.88031325 -1.19071404
[2,] -0.87898023 2.5130196 0.26264050 -0.1234444 0.47744441 0.52823675
[3,] -0.06881968 -0.3491730 -0.05271661 -0.8215817 0.06909143 1.31385898
[4,] 0.21821419 -1.6418237 0.72519896 0.4888030 -1.60208813 -0.32078484
[5,] 0.05217482 1.2454016 -0.69279871 -0.6162439 0.31455865 0.02161988
[,19] [,20]
[1,] 0.4644070 0.1848862
[2,] 0.1895749 0.7812337
[3,] -0.2664125 -0.3193807
[4,] 1.3043832 -0.7354245
[5,] -0.6598695 0.7326437
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 649 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 562 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 2.099735 -0.6707902 0.5336391 -1.265505 0.173558 -0.183494 0.997732
col8 col9 col10 col11 col12 col13 col14
row1 -0.7888802 -1.082417 -1.780818 1.370511 -0.9214593 -0.03553123 1.90139
col15 col16 col17 col18 col19 col20
row1 -0.3778594 -0.6411381 0.4645572 0.7495829 1.291294 -1.250814
> tmp[,"col10"]
col10
row1 -1.7808182
row2 -0.8994180
row3 0.1705633
row4 -1.4288930
row5 -0.3173810
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 2.099735 -0.6707902 0.5336391 -1.2655046 0.173558 -0.18349403 0.9977320
row5 1.025569 0.5535757 1.0325915 -0.9881351 1.701736 0.08890607 -0.1532904
col8 col9 col10 col11 col12 col13
row1 -0.7888802 -1.0824170 -1.780818 1.3705107 -0.9214593 -0.03553123
row5 0.4334217 -0.3218847 -0.317381 -0.1805251 1.1706447 -1.63702352
col14 col15 col16 col17 col18 col19 col20
row1 1.9013895 -0.3778594 -0.6411381 0.4645572 0.7495829 1.291294 -1.2508136
row5 0.8842616 0.8228450 -1.9279070 1.2399365 -0.7002346 -1.107877 -0.7094287
> tmp[,c("col6","col20")]
col6 col20
row1 -0.18349403 -1.2508136
row2 -0.57813042 0.4043822
row3 1.41107353 0.7174174
row4 -0.01993996 1.1378871
row5 0.08890607 -0.7094287
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.18349403 -1.2508136
row5 0.08890607 -0.7094287
>
>
>
>
> 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 51.23999 49.43901 49.39447 51.28619 48.47717 107.5674 49.44156 51.57028
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.64167 48.51767 49.40694 49.58751 51.64818 49.59664 50.26811 49.26162
col17 col18 col19 col20
row1 49.42835 50.03843 50.41507 104.6375
> tmp[,"col10"]
col10
row1 48.51767
row2 28.37321
row3 30.46849
row4 28.53733
row5 50.31827
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.23999 49.43901 49.39447 51.28619 48.47717 107.5674 49.44156 51.57028
row5 48.86193 50.44353 50.51141 51.26254 49.87511 104.9019 48.15934 48.83499
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.64167 48.51767 49.40694 49.58751 51.64818 49.59664 50.26811 49.26162
row5 48.34676 50.31827 51.02562 50.40054 50.88471 50.14180 50.66733 50.29375
col17 col18 col19 col20
row1 49.42835 50.03843 50.41507 104.6375
row5 50.43693 51.10393 49.55977 105.3099
> tmp[,c("col6","col20")]
col6 col20
row1 107.56742 104.63754
row2 75.81961 76.89532
row3 75.50549 74.67868
row4 73.85722 75.94243
row5 104.90193 105.30988
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 107.5674 104.6375
row5 104.9019 105.3099
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 107.5674 104.6375
row5 104.9019 105.3099
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.18107567
[2,] 0.68029742
[3,] -0.01153302
[4,] -0.45507287
[5,] 0.29343682
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.1493130 -0.2769663
[2,] 0.7185010 1.5922335
[3,] -0.8188150 0.2116972
[4,] 0.3689487 -0.3260979
[5,] 0.5258782 2.0949985
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -1.3786525 -0.03540641
[2,] -0.5243525 -2.29456707
[3,] -1.0506973 0.67802280
[4,] 0.9341069 0.33425812
[5,] 0.7422152 0.20045523
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -1.378652
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -1.3786525
[2,] -0.5243525
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -0.5420308 0.9170127 -0.1976849 0.2038823 -0.1101119 1.0086457
row1 0.6945588 0.1083740 -0.7086121 -1.4036111 0.2186149 -0.0664945
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 0.01069464 0.3314567 0.4277793 -0.2851968 1.1677538 0.7806972 0.1369998
row1 -1.70773571 -0.3675059 0.8292294 -0.6813981 0.2050741 0.7103933 0.2619398
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.895002 0.6170978 0.5084375 -0.4559523 0.1875214 0.07348665 1.0509144
row1 2.929948 1.2722841 0.5088256 -0.2744868 -0.2250962 -0.45641282 -0.8508468
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.136894 -2.443038 0.5711891 -0.1257149 1.138541 1.152898 -0.264991
[,8] [,9] [,10]
row2 -2.244521 -2.205006 -0.8350811
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.4122994 -0.1558346 0.3619241 1.512762 1.093492 0.1024715 2.532422
[,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15]
row5 -0.237971 1.23772 1.30083 -1.556619 0.5677463 0.237873 -0.4349232 1.830609
[,16] [,17] [,18] [,19] [,20]
row5 0.5155044 1.297873 0.8103313 -0.2058251 -2.142741
>
>
> 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: 0x6000003ac060>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e914919f476"
[2] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e9147009478"
[3] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e91771376b2"
[4] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e911ed5dd31"
[5] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e916aaccbc7"
[6] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e917676ac87"
[7] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e9169390fd3"
[8] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e91213e1b9d"
[9] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e917486f177"
[10] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e914756f765"
[11] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e911e8c2c7a"
[12] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e914bc0d41"
[13] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e91560a28d4"
[14] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e9134fea26d"
[15] "/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM8e913959bd49"
>
>
> ### 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: 0x6000003b4180>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6000003b4180>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6000003b4180>
> rowMedians(tmp)
[1] 0.064405402 -0.343905879 -0.191910150 0.345962263 -0.446509957
[6] -0.348866611 0.314337430 -0.083121815 -0.006621298 0.232675248
[11] 0.578708850 0.110779589 -0.117130199 0.111134174 -0.412342090
[16] 0.291372257 -0.006315272 -0.490695931 0.131879509 -0.074855179
[21] 0.159157672 -0.065081149 -0.306648406 -0.355537260 -0.304260379
[26] -0.016257110 0.227252542 0.198934755 -0.054932570 0.467664983
[31] -0.315098806 -0.649161782 0.174768292 -0.016937004 0.009305676
[36] 0.149490414 -0.441812888 0.199055142 -0.225628989 -0.559878203
[41] 0.449989310 -0.578294482 -0.370889289 0.335935203 -0.296167330
[46] 0.060608863 -0.627612405 -0.192392794 -0.428741257 -0.090071567
[51] -0.237183279 0.129453035 -0.090585756 0.020291660 0.190619480
[56] 0.134314069 0.072142661 -0.139080822 -0.066340680 0.210756077
[61] -0.196222358 -0.425620954 -0.261591990 -0.106161192 0.107630525
[66] 0.422065109 -0.169848970 0.035621235 0.497203117 0.226209710
[71] -0.005213979 -0.159139164 -0.593623188 -0.120372547 0.382859377
[76] 0.350113894 -0.256988199 0.482118401 -0.047962852 -0.308333968
[81] -0.046661844 0.267587952 -0.244884826 0.405160512 -0.261368585
[86] 0.131231963 -0.208707910 0.551256380 0.343684882 -0.477003241
[91] -0.468648822 -0.493579014 -0.187104108 0.084758084 0.256817978
[96] -0.652841992 0.195450895 0.270958010 -0.199946790 -0.055426158
[101] 0.236884144 -0.131779013 0.061388060 0.673628101 0.065975425
[106] 0.213130508 0.368038642 -0.124239297 0.207614605 0.033111959
[111] -0.025853999 -0.518873690 0.331376363 0.236064054 -0.307956746
[116] 0.344691362 -0.131335409 -0.257405798 -0.031828487 -0.244526266
[121] -0.222104726 -0.154679631 -0.181181857 0.261007734 -0.181019260
[126] 0.404753681 0.419645130 0.381796699 -0.374928145 0.078929190
[131] 0.166471192 0.294559314 0.259916966 0.085285987 -0.671198813
[136] 0.631321858 0.088491652 0.492966194 -0.198473462 0.022234540
[141] 0.608094821 -0.434329552 0.842804161 -0.097911550 -0.203057554
[146] -0.163730163 -0.210650719 0.267520805 -0.103825583 -0.523971425
[151] -0.184938277 0.106691146 0.014746943 0.545457500 -0.521402831
[156] -0.339168727 0.242943353 0.356488949 0.544498054 -0.046681707
[161] 0.064993673 -0.271331425 0.398207091 0.459111153 -0.327969931
[166] -0.164961489 -0.064585404 -0.002072115 0.122297283 0.736102708
[171] -0.095543933 0.198917837 -0.343259262 -0.277372995 -0.060524665
[176] 0.081959227 0.232197249 -0.134030790 0.520780753 -0.430217933
[181] -0.283723809 0.031160554 0.305115305 0.264851156 0.257492658
[186] 0.033059910 -0.083007751 0.412048286 0.500427502 0.226852819
[191] 0.142662914 -0.003888310 0.019319584 -0.350843475 0.030920110
[196] 0.082891159 0.060661463 -0.141891388 -0.132153192 0.255401147
[201] 0.183662323 -0.390168397 0.076730551 0.115314791 0.294853069
[206] 0.584298279 -0.045604438 0.268800847 -0.152869256 0.387016769
[211] 0.570144720 0.069463287 -0.400394670 -0.765084379 -0.221523999
[216] -0.029792298 0.067396655 1.000066029 -0.324600797 -0.073595318
[221] 0.645938211 0.514454764 -0.532547107 0.462406804 0.089788576
[226] -0.185293189 -0.214407144 -0.217300736 0.020418112 0.043632046
>
> proc.time()
user system elapsed
2.739 16.734 20.148
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
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: 0x600001428120>
> .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: 0x600001428120>
> .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: 0x600001428120>
> .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: 0x600001428120>
> 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: 0x600001450000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600001450000>
> .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: 0x600001450000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600001450000>
> .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: 0x600001450000>
> 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: 0x600001454000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600001454000>
> .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: 0x600001454000>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600001454000>
> .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: 0x600001454000>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600001454000>
> .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: 0x600001454000>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600001454000>
> .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: 0x600001454000>
> 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: 0x600001468000>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600001468000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600001468000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600001468000>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile929649cd9245" "BufferedMatrixFile9296573e15dd"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile929649cd9245" "BufferedMatrixFile9296573e15dd"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600001438240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600001438240>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600001438240>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600001438240>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600001438240>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600001438240>
> .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: 0x60000146c000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60000146c000>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x60000146c000>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x60000146c000>
> 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: 0x600001460000>
> .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: 0x600001460000>
> rm(P)
>
> proc.time()
user system elapsed
0.362 0.167 0.533
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
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
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.352 0.098 0.438