Ben Bolstad
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_20 |
| git_last_commit: 32b6f6a |
| git_last_commit_date: 2024-10-29 09:27:20 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:06 -0400 (Mon, 10 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| 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 251/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.70.0 (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 | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.70.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.70.0.tar.gz |
| StartedAt: 2025-03-06 23:56:02 -0500 (Thu, 06 Mar 2025) |
| EndedAt: 2025-03-06 23:59:02 -0500 (Thu, 06 Mar 2025) |
| EllapsedTime: 180.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.70.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BufferedMatrix/DESCRIPTION' ... OK
* this is package 'BufferedMatrix' version '1.70.0'
* 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 whether package 'BufferedMatrix' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/BufferedMatrix/libs/x64/BufferedMatrix.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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: 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BufferedMatrix' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function 'dbm_ReadOnlyMode':
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: 'sort_double' defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
gcc -shared -s -static-libgcc -o BufferedMatrix.dll tmp.def RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs/x64
** 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
** 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 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
0.34 0.10 0.96
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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] "F:/biocbuild/bbs-3.20-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) max used (Mb)
Ncells 467958 25.0 1020317 54.5 633411 33.9
Vcells 853510 6.6 8388608 64.0 2003128 15.3
>
>
>
>
> ##
> ## 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] "Thu Mar 6 23:56:33 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] "Thu Mar 6 23:56:36 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: 0x000002a20faf88f0>
>
>
>
> 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] "Thu Mar 6 23:57:13 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] "Thu Mar 6 23:57:26 2025"
>
> ColMode(tmp2)
<pointer: 0x000002a20faf88f0>
>
>
>
> ### 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,] 101.4928687 1.610524706 -0.2008352 1.378384
[2,] 0.9011104 0.053119340 2.2415008 1.050223
[3,] 1.3390736 0.563749339 -0.1291658 1.187617
[4,] 0.4491462 -0.001060543 -0.2354202 1.108382
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-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,] 101.4928687 1.610524706 0.2008352 1.378384
[2,] 0.9011104 0.053119340 2.2415008 1.050223
[3,] 1.3390736 0.563749339 0.1291658 1.187617
[4,] 0.4491462 0.001060543 0.2354202 1.108382
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-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,] 10.0743669 1.26906450 0.4481464 1.174046
[2,] 0.9492684 0.23047633 1.4971642 1.024804
[3,] 1.1571835 0.75083243 0.3593964 1.089778
[4,] 0.6701837 0.03256597 0.4852012 1.052797
>
> 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: F:/biocbuild/bbs-3.20-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,] 227.23654 39.30117 29.68230 38.11885
[2,] 35.39379 27.35788 42.21314 36.29826
[3,] 37.91091 33.07207 28.72313 37.08540
[4,] 32.15098 25.32672 30.08743 36.63636
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x000002a20faf8830>
> exp(tmp5)
<pointer: 0x000002a20faf8830>
> log(tmp5,2)
<pointer: 0x000002a20faf8830>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 472.9631
> Min(tmp5)
[1] 52.71425
> mean(tmp5)
[1] 73.86747
> Sum(tmp5)
[1] 14773.49
> Var(tmp5)
[1] 878.3357
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.38645 69.92291 69.06527 70.35634 74.48849 70.34166 69.61253 71.50126
[9] 77.74940 75.25041
> rowSums(tmp5)
[1] 1807.729 1398.458 1381.305 1407.127 1489.770 1406.833 1392.251 1430.025
[9] 1554.988 1505.008
> rowVars(tmp5)
[1] 8205.63119 77.17295 73.92760 73.85596 44.14218 63.17953
[7] 47.30930 86.81499 61.73768 68.45180
> rowSd(tmp5)
[1] 90.584939 8.784814 8.598116 8.593949 6.643958 7.948555 6.878176
[8] 9.317456 7.857333 8.273560
> rowMax(tmp5)
[1] 472.96308 87.86113 92.48611 87.82072 89.53232 84.10681 80.04681
[8] 88.11167 93.87051 87.79998
> rowMin(tmp5)
[1] 53.89692 53.82736 57.62079 52.71425 62.18362 57.40800 54.28710 54.73569
[9] 61.34373 58.23171
>
> colMeans(tmp5)
[1] 114.15087 66.98797 70.80075 75.58120 71.04142 70.05998 73.79459
[8] 71.09664 72.81966 76.34980 75.00840 73.91629 71.51291 72.53646
[15] 68.64084 75.42942 72.49003 67.45882 72.27966 65.39378
> colSums(tmp5)
[1] 1141.5087 669.8797 708.0075 755.8120 710.4142 700.5998 737.9459
[8] 710.9664 728.1966 763.4980 750.0840 739.1629 715.1291 725.3646
[15] 686.4084 754.2942 724.9003 674.5882 722.7966 653.9378
> colVars(tmp5)
[1] 15935.24778 110.16347 123.15735 32.38736 100.12598 104.92071
[7] 89.78113 38.89720 75.69895 56.33444 42.23894 97.17173
[13] 51.79724 92.83906 42.67368 30.56450 43.87723 105.61793
[19] 54.52687 109.04741
> colSd(tmp5)
[1] 126.234891 10.495878 11.097628 5.690989 10.006297 10.243081
[7] 9.475291 6.236762 8.700514 7.505627 6.499149 9.857572
[13] 7.197030 9.635303 6.532509 5.528517 6.623989 10.277058
[19] 7.384231 10.442577
> colMax(tmp5)
[1] 472.96308 86.55802 87.86113 82.79867 89.53232 92.48611 87.82072
[8] 80.09753 84.66379 88.11167 84.69792 93.87051 82.32855 94.12005
[15] 76.02159 83.37781 80.80131 87.79998 81.24089 82.20272
> colMin(tmp5)
[1] 62.57135 52.71425 59.78343 62.51614 57.83613 54.28710 53.82736 61.42095
[9] 59.13750 66.48511 64.59845 62.59100 63.14294 60.15449 58.23171 66.57492
[17] 58.84211 54.79283 57.62079 53.89692
>
>
> ### 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] 90.38645 69.92291 69.06527 70.35634 74.48849 70.34166 NA 71.50126
[9] 77.74940 75.25041
> rowSums(tmp5)
[1] 1807.729 1398.458 1381.305 1407.127 1489.770 1406.833 NA 1430.025
[9] 1554.988 1505.008
> rowVars(tmp5)
[1] 8205.63119 77.17295 73.92760 73.85596 44.14218 63.17953
[7] 49.62654 86.81499 61.73768 68.45180
> rowSd(tmp5)
[1] 90.584939 8.784814 8.598116 8.593949 6.643958 7.948555 7.044611
[8] 9.317456 7.857333 8.273560
> rowMax(tmp5)
[1] 472.96308 87.86113 92.48611 87.82072 89.53232 84.10681 NA
[8] 88.11167 93.87051 87.79998
> rowMin(tmp5)
[1] 53.89692 53.82736 57.62079 52.71425 62.18362 57.40800 NA 54.73569
[9] 61.34373 58.23171
>
> colMeans(tmp5)
[1] 114.15087 66.98797 NA 75.58120 71.04142 70.05998 73.79459
[8] 71.09664 72.81966 76.34980 75.00840 73.91629 71.51291 72.53646
[15] 68.64084 75.42942 72.49003 67.45882 72.27966 65.39378
> colSums(tmp5)
[1] 1141.5087 669.8797 NA 755.8120 710.4142 700.5998 737.9459
[8] 710.9664 728.1966 763.4980 750.0840 739.1629 715.1291 725.3646
[15] 686.4084 754.2942 724.9003 674.5882 722.7966 653.9378
> colVars(tmp5)
[1] 15935.24778 110.16347 NA 32.38736 100.12598 104.92071
[7] 89.78113 38.89720 75.69895 56.33444 42.23894 97.17173
[13] 51.79724 92.83906 42.67368 30.56450 43.87723 105.61793
[19] 54.52687 109.04741
> colSd(tmp5)
[1] 126.234891 10.495878 NA 5.690989 10.006297 10.243081
[7] 9.475291 6.236762 8.700514 7.505627 6.499149 9.857572
[13] 7.197030 9.635303 6.532509 5.528517 6.623989 10.277058
[19] 7.384231 10.442577
> colMax(tmp5)
[1] 472.96308 86.55802 NA 82.79867 89.53232 92.48611 87.82072
[8] 80.09753 84.66379 88.11167 84.69792 93.87051 82.32855 94.12005
[15] 76.02159 83.37781 80.80131 87.79998 81.24089 82.20272
> colMin(tmp5)
[1] 62.57135 52.71425 NA 62.51614 57.83613 54.28710 53.82736 61.42095
[9] 59.13750 66.48511 64.59845 62.59100 63.14294 60.15449 58.23171 66.57492
[17] 58.84211 54.79283 57.62079 53.89692
>
> Max(tmp5,na.rm=TRUE)
[1] 472.9631
> Min(tmp5,na.rm=TRUE)
[1] 52.71425
> mean(tmp5,na.rm=TRUE)
[1] 73.87727
> Sum(tmp5,na.rm=TRUE)
[1] 14701.58
> Var(tmp5,na.rm=TRUE)
[1] 882.7524
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.38645 69.92291 69.06527 70.35634 74.48849 70.34166 69.49115 71.50126
[9] 77.74940 75.25041
> rowSums(tmp5,na.rm=TRUE)
[1] 1807.729 1398.458 1381.305 1407.127 1489.770 1406.833 1320.332 1430.025
[9] 1554.988 1505.008
> rowVars(tmp5,na.rm=TRUE)
[1] 8205.63119 77.17295 73.92760 73.85596 44.14218 63.17953
[7] 49.62654 86.81499 61.73768 68.45180
> rowSd(tmp5,na.rm=TRUE)
[1] 90.584939 8.784814 8.598116 8.593949 6.643958 7.948555 7.044611
[8] 9.317456 7.857333 8.273560
> rowMax(tmp5,na.rm=TRUE)
[1] 472.96308 87.86113 92.48611 87.82072 89.53232 84.10681 80.04681
[8] 88.11167 93.87051 87.79998
> rowMin(tmp5,na.rm=TRUE)
[1] 53.89692 53.82736 57.62079 52.71425 62.18362 57.40800 54.28710 54.73569
[9] 61.34373 58.23171
>
> colMeans(tmp5,na.rm=TRUE)
[1] 114.15087 66.98797 70.67652 75.58120 71.04142 70.05998 73.79459
[8] 71.09664 72.81966 76.34980 75.00840 73.91629 71.51291 72.53646
[15] 68.64084 75.42942 72.49003 67.45882 72.27966 65.39378
> colSums(tmp5,na.rm=TRUE)
[1] 1141.5087 669.8797 636.0886 755.8120 710.4142 700.5998 737.9459
[8] 710.9664 728.1966 763.4980 750.0840 739.1629 715.1291 725.3646
[15] 686.4084 754.2942 724.9003 674.5882 722.7966 653.9378
> colVars(tmp5,na.rm=TRUE)
[1] 15935.24778 110.16347 138.37839 32.38736 100.12598 104.92071
[7] 89.78113 38.89720 75.69895 56.33444 42.23894 97.17173
[13] 51.79724 92.83906 42.67368 30.56450 43.87723 105.61793
[19] 54.52687 109.04741
> colSd(tmp5,na.rm=TRUE)
[1] 126.234891 10.495878 11.763435 5.690989 10.006297 10.243081
[7] 9.475291 6.236762 8.700514 7.505627 6.499149 9.857572
[13] 7.197030 9.635303 6.532509 5.528517 6.623989 10.277058
[19] 7.384231 10.442577
> colMax(tmp5,na.rm=TRUE)
[1] 472.96308 86.55802 87.86113 82.79867 89.53232 92.48611 87.82072
[8] 80.09753 84.66379 88.11167 84.69792 93.87051 82.32855 94.12005
[15] 76.02159 83.37781 80.80131 87.79998 81.24089 82.20272
> colMin(tmp5,na.rm=TRUE)
[1] 62.57135 52.71425 59.78343 62.51614 57.83613 54.28710 53.82736 61.42095
[9] 59.13750 66.48511 64.59845 62.59100 63.14294 60.15449 58.23171 66.57492
[17] 58.84211 54.79283 57.62079 53.89692
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.38645 69.92291 69.06527 70.35634 74.48849 70.34166 NaN 71.50126
[9] 77.74940 75.25041
> rowSums(tmp5,na.rm=TRUE)
[1] 1807.729 1398.458 1381.305 1407.127 1489.770 1406.833 0.000 1430.025
[9] 1554.988 1505.008
> rowVars(tmp5,na.rm=TRUE)
[1] 8205.63119 77.17295 73.92760 73.85596 44.14218 63.17953
[7] NA 86.81499 61.73768 68.45180
> rowSd(tmp5,na.rm=TRUE)
[1] 90.584939 8.784814 8.598116 8.593949 6.643958 7.948555 NA
[8] 9.317456 7.857333 8.273560
> rowMax(tmp5,na.rm=TRUE)
[1] 472.96308 87.86113 92.48611 87.82072 89.53232 84.10681 NA
[8] 88.11167 93.87051 87.79998
> rowMin(tmp5,na.rm=TRUE)
[1] 53.89692 53.82736 57.62079 52.71425 62.18362 57.40800 NA 54.73569
[9] 61.34373 58.23171
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 118.81167 67.44497 NaN 76.05298 72.50867 71.81252 74.05430
[8] 71.47565 73.56550 75.93903 76.01311 73.90576 72.19535 72.08594
[15] 67.97479 76.41325 71.71977 66.92366 71.66904 65.56242
> colSums(tmp5,na.rm=TRUE)
[1] 1069.3050 607.0047 0.0000 684.4768 652.5780 646.3127 666.4887
[8] 643.2808 662.0895 683.4512 684.1180 665.1518 649.7581 648.7734
[15] 611.7731 687.7193 645.4780 602.3130 645.0214 590.0618
> colVars(tmp5,na.rm=TRUE)
[1] 17682.76926 121.58439 NA 33.93186 88.42235 83.48249
[7] 100.24499 42.14329 78.90318 61.47793 36.16258 109.31695
[13] 53.03245 102.16053 43.01726 23.49587 42.68738 115.59826
[19] 57.14809 122.35837
> colSd(tmp5,na.rm=TRUE)
[1] 132.976574 11.026531 NA 5.825106 9.403316 9.136875
[7] 10.012242 6.491786 8.882746 7.840786 6.013533 10.455475
[13] 7.282339 10.107449 6.558754 4.847254 6.533558 10.751663
[19] 7.559635 11.061572
> colMax(tmp5,na.rm=TRUE)
[1] 472.96308 86.55802 -Inf 82.79867 89.53232 92.48611 87.82072
[8] 80.09753 84.66379 88.11167 84.69792 93.87051 82.32855 94.12005
[15] 76.02159 83.37781 80.80131 87.79998 81.24089 82.20272
> colMin(tmp5,na.rm=TRUE)
[1] 62.57135 52.71425 Inf 62.51614 62.13630 63.85034 53.82736 61.42095
[9] 59.13750 66.48511 64.59845 62.59100 63.14294 60.15449 58.23171 71.61941
[17] 58.84211 54.79283 57.62079 53.89692
>
>
>
>
> 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] 315.2490 190.2113 189.3749 124.2289 301.8168 180.1091 228.6564 185.6866
[9] 204.3364 128.1979
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 315.2490 190.2113 189.3749 124.2289 301.8168 180.1091 228.6564 185.6866
[9] 204.3364 128.1979
>
>
>
> 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] -1.136868e-13 5.684342e-14 2.273737e-13 1.705303e-13 0.000000e+00
[6] 2.842171e-14 -1.136868e-13 2.842171e-14 0.000000e+00 -1.421085e-14
[11] 0.000000e+00 2.842171e-14 2.273737e-13 0.000000e+00 1.136868e-13
[16] 2.842171e-14 8.526513e-14 5.684342e-14 0.000000e+00 -1.421085e-13
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
5 7
2 10
10 20
9 17
10 7
8 12
5 12
5 17
8 1
2 12
3 15
9 18
2 12
1 10
3 7
7 7
6 6
6 9
7 16
9 20
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] 2.213972
> Min(tmp)
[1] -2.437927
> mean(tmp)
[1] -0.03904419
> Sum(tmp)
[1] -3.904419
> Var(tmp)
[1] 1.105727
>
> rowMeans(tmp)
[1] -0.03904419
> rowSums(tmp)
[1] -3.904419
> rowVars(tmp)
[1] 1.105727
> rowSd(tmp)
[1] 1.051535
> rowMax(tmp)
[1] 2.213972
> rowMin(tmp)
[1] -2.437927
>
> colMeans(tmp)
[1] -0.49709446 1.80213363 0.66510928 -0.25530971 -0.46001834 0.28270168
[7] 0.29971260 -1.51491206 -0.59757300 -0.50116824 0.16182171 0.79852787
[13] 1.18044013 -2.36673799 -1.46774552 0.37305487 -1.95766949 1.62852403
[19] -0.78699993 0.85035543 0.89666375 1.64959768 -1.37041163 -0.03400306
[25] -0.83501958 -0.89025348 -2.09799180 1.07073175 -0.61171733 -1.83333325
[31] -0.89387678 1.04588947 -0.55298505 -0.87064707 0.78339839 1.47279734
[37] 0.06037287 1.08979999 -0.12739297 1.37341155 -1.71688758 -0.33593832
[43] -0.12337566 0.77825810 -0.62883168 -0.70194292 -0.14330863 -2.25373167
[49] 0.57315158 -0.05325723 -0.41699703 1.18722721 0.45943691 -0.06565415
[55] -0.20490164 -0.76449273 0.40745803 1.53100229 0.23797844 0.60676248
[61] -0.02632623 0.45210331 0.11097049 0.50722145 0.64276992 1.00507589
[67] -0.20056347 1.17154049 0.49891384 0.50048046 -1.49906497 1.21097985
[73] 0.34565252 -1.08773110 1.21377369 0.52088898 -0.20778892 0.10629343
[79] 0.71263439 -0.59368591 -1.43476946 -0.45415856 2.21397242 -0.27255473
[85] -0.71620685 1.66742197 -0.46858112 -0.40166341 0.37537839 -1.08679665
[91] 0.48366736 0.35322343 -2.43792676 2.18908626 -0.53908616 0.91272221
[97] -1.84007478 -0.69879750 -2.04686934 -0.42068249
> colSums(tmp)
[1] -0.49709446 1.80213363 0.66510928 -0.25530971 -0.46001834 0.28270168
[7] 0.29971260 -1.51491206 -0.59757300 -0.50116824 0.16182171 0.79852787
[13] 1.18044013 -2.36673799 -1.46774552 0.37305487 -1.95766949 1.62852403
[19] -0.78699993 0.85035543 0.89666375 1.64959768 -1.37041163 -0.03400306
[25] -0.83501958 -0.89025348 -2.09799180 1.07073175 -0.61171733 -1.83333325
[31] -0.89387678 1.04588947 -0.55298505 -0.87064707 0.78339839 1.47279734
[37] 0.06037287 1.08979999 -0.12739297 1.37341155 -1.71688758 -0.33593832
[43] -0.12337566 0.77825810 -0.62883168 -0.70194292 -0.14330863 -2.25373167
[49] 0.57315158 -0.05325723 -0.41699703 1.18722721 0.45943691 -0.06565415
[55] -0.20490164 -0.76449273 0.40745803 1.53100229 0.23797844 0.60676248
[61] -0.02632623 0.45210331 0.11097049 0.50722145 0.64276992 1.00507589
[67] -0.20056347 1.17154049 0.49891384 0.50048046 -1.49906497 1.21097985
[73] 0.34565252 -1.08773110 1.21377369 0.52088898 -0.20778892 0.10629343
[79] 0.71263439 -0.59368591 -1.43476946 -0.45415856 2.21397242 -0.27255473
[85] -0.71620685 1.66742197 -0.46858112 -0.40166341 0.37537839 -1.08679665
[91] 0.48366736 0.35322343 -2.43792676 2.18908626 -0.53908616 0.91272221
[97] -1.84007478 -0.69879750 -2.04686934 -0.42068249
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.49709446 1.80213363 0.66510928 -0.25530971 -0.46001834 0.28270168
[7] 0.29971260 -1.51491206 -0.59757300 -0.50116824 0.16182171 0.79852787
[13] 1.18044013 -2.36673799 -1.46774552 0.37305487 -1.95766949 1.62852403
[19] -0.78699993 0.85035543 0.89666375 1.64959768 -1.37041163 -0.03400306
[25] -0.83501958 -0.89025348 -2.09799180 1.07073175 -0.61171733 -1.83333325
[31] -0.89387678 1.04588947 -0.55298505 -0.87064707 0.78339839 1.47279734
[37] 0.06037287 1.08979999 -0.12739297 1.37341155 -1.71688758 -0.33593832
[43] -0.12337566 0.77825810 -0.62883168 -0.70194292 -0.14330863 -2.25373167
[49] 0.57315158 -0.05325723 -0.41699703 1.18722721 0.45943691 -0.06565415
[55] -0.20490164 -0.76449273 0.40745803 1.53100229 0.23797844 0.60676248
[61] -0.02632623 0.45210331 0.11097049 0.50722145 0.64276992 1.00507589
[67] -0.20056347 1.17154049 0.49891384 0.50048046 -1.49906497 1.21097985
[73] 0.34565252 -1.08773110 1.21377369 0.52088898 -0.20778892 0.10629343
[79] 0.71263439 -0.59368591 -1.43476946 -0.45415856 2.21397242 -0.27255473
[85] -0.71620685 1.66742197 -0.46858112 -0.40166341 0.37537839 -1.08679665
[91] 0.48366736 0.35322343 -2.43792676 2.18908626 -0.53908616 0.91272221
[97] -1.84007478 -0.69879750 -2.04686934 -0.42068249
> colMin(tmp)
[1] -0.49709446 1.80213363 0.66510928 -0.25530971 -0.46001834 0.28270168
[7] 0.29971260 -1.51491206 -0.59757300 -0.50116824 0.16182171 0.79852787
[13] 1.18044013 -2.36673799 -1.46774552 0.37305487 -1.95766949 1.62852403
[19] -0.78699993 0.85035543 0.89666375 1.64959768 -1.37041163 -0.03400306
[25] -0.83501958 -0.89025348 -2.09799180 1.07073175 -0.61171733 -1.83333325
[31] -0.89387678 1.04588947 -0.55298505 -0.87064707 0.78339839 1.47279734
[37] 0.06037287 1.08979999 -0.12739297 1.37341155 -1.71688758 -0.33593832
[43] -0.12337566 0.77825810 -0.62883168 -0.70194292 -0.14330863 -2.25373167
[49] 0.57315158 -0.05325723 -0.41699703 1.18722721 0.45943691 -0.06565415
[55] -0.20490164 -0.76449273 0.40745803 1.53100229 0.23797844 0.60676248
[61] -0.02632623 0.45210331 0.11097049 0.50722145 0.64276992 1.00507589
[67] -0.20056347 1.17154049 0.49891384 0.50048046 -1.49906497 1.21097985
[73] 0.34565252 -1.08773110 1.21377369 0.52088898 -0.20778892 0.10629343
[79] 0.71263439 -0.59368591 -1.43476946 -0.45415856 2.21397242 -0.27255473
[85] -0.71620685 1.66742197 -0.46858112 -0.40166341 0.37537839 -1.08679665
[91] 0.48366736 0.35322343 -2.43792676 2.18908626 -0.53908616 0.91272221
[97] -1.84007478 -0.69879750 -2.04686934 -0.42068249
> colMedians(tmp)
[1] -0.49709446 1.80213363 0.66510928 -0.25530971 -0.46001834 0.28270168
[7] 0.29971260 -1.51491206 -0.59757300 -0.50116824 0.16182171 0.79852787
[13] 1.18044013 -2.36673799 -1.46774552 0.37305487 -1.95766949 1.62852403
[19] -0.78699993 0.85035543 0.89666375 1.64959768 -1.37041163 -0.03400306
[25] -0.83501958 -0.89025348 -2.09799180 1.07073175 -0.61171733 -1.83333325
[31] -0.89387678 1.04588947 -0.55298505 -0.87064707 0.78339839 1.47279734
[37] 0.06037287 1.08979999 -0.12739297 1.37341155 -1.71688758 -0.33593832
[43] -0.12337566 0.77825810 -0.62883168 -0.70194292 -0.14330863 -2.25373167
[49] 0.57315158 -0.05325723 -0.41699703 1.18722721 0.45943691 -0.06565415
[55] -0.20490164 -0.76449273 0.40745803 1.53100229 0.23797844 0.60676248
[61] -0.02632623 0.45210331 0.11097049 0.50722145 0.64276992 1.00507589
[67] -0.20056347 1.17154049 0.49891384 0.50048046 -1.49906497 1.21097985
[73] 0.34565252 -1.08773110 1.21377369 0.52088898 -0.20778892 0.10629343
[79] 0.71263439 -0.59368591 -1.43476946 -0.45415856 2.21397242 -0.27255473
[85] -0.71620685 1.66742197 -0.46858112 -0.40166341 0.37537839 -1.08679665
[91] 0.48366736 0.35322343 -2.43792676 2.18908626 -0.53908616 0.91272221
[97] -1.84007478 -0.69879750 -2.04686934 -0.42068249
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.4970945 1.802134 0.6651093 -0.2553097 -0.4600183 0.2827017 0.2997126
[2,] -0.4970945 1.802134 0.6651093 -0.2553097 -0.4600183 0.2827017 0.2997126
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.514912 -0.597573 -0.5011682 0.1618217 0.7985279 1.18044 -2.366738
[2,] -1.514912 -0.597573 -0.5011682 0.1618217 0.7985279 1.18044 -2.366738
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.467746 0.3730549 -1.957669 1.628524 -0.7869999 0.8503554 0.8966637
[2,] -1.467746 0.3730549 -1.957669 1.628524 -0.7869999 0.8503554 0.8966637
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.649598 -1.370412 -0.03400306 -0.8350196 -0.8902535 -2.097992 1.070732
[2,] 1.649598 -1.370412 -0.03400306 -0.8350196 -0.8902535 -2.097992 1.070732
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.6117173 -1.833333 -0.8938768 1.045889 -0.552985 -0.8706471 0.7833984
[2,] -0.6117173 -1.833333 -0.8938768 1.045889 -0.552985 -0.8706471 0.7833984
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 1.472797 0.06037287 1.0898 -0.127393 1.373412 -1.716888 -0.3359383
[2,] 1.472797 0.06037287 1.0898 -0.127393 1.373412 -1.716888 -0.3359383
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.1233757 0.7782581 -0.6288317 -0.7019429 -0.1433086 -2.253732 0.5731516
[2,] -0.1233757 0.7782581 -0.6288317 -0.7019429 -0.1433086 -2.253732 0.5731516
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.05325723 -0.416997 1.187227 0.4594369 -0.06565415 -0.2049016 -0.7644927
[2,] -0.05325723 -0.416997 1.187227 0.4594369 -0.06565415 -0.2049016 -0.7644927
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.407458 1.531002 0.2379784 0.6067625 -0.02632623 0.4521033 0.1109705
[2,] 0.407458 1.531002 0.2379784 0.6067625 -0.02632623 0.4521033 0.1109705
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.5072215 0.6427699 1.005076 -0.2005635 1.17154 0.4989138 0.5004805
[2,] 0.5072215 0.6427699 1.005076 -0.2005635 1.17154 0.4989138 0.5004805
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.499065 1.21098 0.3456525 -1.087731 1.213774 0.520889 -0.2077889
[2,] -1.499065 1.21098 0.3456525 -1.087731 1.213774 0.520889 -0.2077889
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.1062934 0.7126344 -0.5936859 -1.434769 -0.4541586 2.213972 -0.2725547
[2,] 0.1062934 0.7126344 -0.5936859 -1.434769 -0.4541586 2.213972 -0.2725547
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.7162068 1.667422 -0.4685811 -0.4016634 0.3753784 -1.086797 0.4836674
[2,] -0.7162068 1.667422 -0.4685811 -0.4016634 0.3753784 -1.086797 0.4836674
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.3532234 -2.437927 2.189086 -0.5390862 0.9127222 -1.840075 -0.6987975
[2,] 0.3532234 -2.437927 2.189086 -0.5390862 0.9127222 -1.840075 -0.6987975
[,99] [,100]
[1,] -2.046869 -0.4206825
[2,] -2.046869 -0.4206825
>
>
> Max(tmp2)
[1] 2.531138
> Min(tmp2)
[1] -2.740722
> mean(tmp2)
[1] 0.06458952
> Sum(tmp2)
[1] 6.458952
> Var(tmp2)
[1] 1.301657
>
> rowMeans(tmp2)
[1] -0.214390412 -1.512236710 -1.424863301 -0.362960454 0.010814792
[6] -2.532576079 -0.538321826 0.513024833 0.370494186 0.256686215
[11] 1.363535717 -1.654903308 -0.290741939 1.590603096 -0.735539960
[16] -0.121696778 0.902346386 1.334482913 -0.184915290 1.590148039
[21] 1.668318969 0.637403479 0.238308353 0.919540835 -2.462816314
[26] 0.961637246 1.053173586 0.002478483 1.121295436 -0.163061618
[31] -0.023343344 -1.010626793 0.968536782 -1.516041912 -0.601715686
[36] 0.588050589 0.710272721 -1.003722184 -0.648256257 -1.191980360
[41] 1.899844905 0.198478937 -1.445815729 0.690712250 -0.436857020
[46] -0.534486386 -0.313324758 -0.276687003 1.023069794 -1.411752763
[51] -0.331678662 0.774125053 -0.223915972 0.998837483 0.941045306
[56] 1.516789997 -2.740722269 -1.182181952 0.340606388 -0.653233326
[61] 1.125131937 1.597410034 0.184672134 1.961180314 -1.795675006
[66] 2.531138430 0.458771373 -0.309086264 -0.633556120 -0.805153894
[71] -0.349900686 0.620750298 -1.585876391 0.991386635 0.926005372
[76] 1.185653376 0.584261130 -0.977868026 0.415175066 -2.434317889
[81] -1.633886555 -0.159227845 0.801936819 2.233942568 1.359429992
[86] -0.779266166 -0.689622846 -0.504849076 0.447207383 2.151205026
[91] 0.591782352 -1.336806360 0.523272755 2.041880828 -1.233704102
[96] 0.127226816 0.705465704 -0.072668606 -0.326985798 1.083221358
> rowSums(tmp2)
[1] -0.214390412 -1.512236710 -1.424863301 -0.362960454 0.010814792
[6] -2.532576079 -0.538321826 0.513024833 0.370494186 0.256686215
[11] 1.363535717 -1.654903308 -0.290741939 1.590603096 -0.735539960
[16] -0.121696778 0.902346386 1.334482913 -0.184915290 1.590148039
[21] 1.668318969 0.637403479 0.238308353 0.919540835 -2.462816314
[26] 0.961637246 1.053173586 0.002478483 1.121295436 -0.163061618
[31] -0.023343344 -1.010626793 0.968536782 -1.516041912 -0.601715686
[36] 0.588050589 0.710272721 -1.003722184 -0.648256257 -1.191980360
[41] 1.899844905 0.198478937 -1.445815729 0.690712250 -0.436857020
[46] -0.534486386 -0.313324758 -0.276687003 1.023069794 -1.411752763
[51] -0.331678662 0.774125053 -0.223915972 0.998837483 0.941045306
[56] 1.516789997 -2.740722269 -1.182181952 0.340606388 -0.653233326
[61] 1.125131937 1.597410034 0.184672134 1.961180314 -1.795675006
[66] 2.531138430 0.458771373 -0.309086264 -0.633556120 -0.805153894
[71] -0.349900686 0.620750298 -1.585876391 0.991386635 0.926005372
[76] 1.185653376 0.584261130 -0.977868026 0.415175066 -2.434317889
[81] -1.633886555 -0.159227845 0.801936819 2.233942568 1.359429992
[86] -0.779266166 -0.689622846 -0.504849076 0.447207383 2.151205026
[91] 0.591782352 -1.336806360 0.523272755 2.041880828 -1.233704102
[96] 0.127226816 0.705465704 -0.072668606 -0.326985798 1.083221358
> 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] -0.214390412 -1.512236710 -1.424863301 -0.362960454 0.010814792
[6] -2.532576079 -0.538321826 0.513024833 0.370494186 0.256686215
[11] 1.363535717 -1.654903308 -0.290741939 1.590603096 -0.735539960
[16] -0.121696778 0.902346386 1.334482913 -0.184915290 1.590148039
[21] 1.668318969 0.637403479 0.238308353 0.919540835 -2.462816314
[26] 0.961637246 1.053173586 0.002478483 1.121295436 -0.163061618
[31] -0.023343344 -1.010626793 0.968536782 -1.516041912 -0.601715686
[36] 0.588050589 0.710272721 -1.003722184 -0.648256257 -1.191980360
[41] 1.899844905 0.198478937 -1.445815729 0.690712250 -0.436857020
[46] -0.534486386 -0.313324758 -0.276687003 1.023069794 -1.411752763
[51] -0.331678662 0.774125053 -0.223915972 0.998837483 0.941045306
[56] 1.516789997 -2.740722269 -1.182181952 0.340606388 -0.653233326
[61] 1.125131937 1.597410034 0.184672134 1.961180314 -1.795675006
[66] 2.531138430 0.458771373 -0.309086264 -0.633556120 -0.805153894
[71] -0.349900686 0.620750298 -1.585876391 0.991386635 0.926005372
[76] 1.185653376 0.584261130 -0.977868026 0.415175066 -2.434317889
[81] -1.633886555 -0.159227845 0.801936819 2.233942568 1.359429992
[86] -0.779266166 -0.689622846 -0.504849076 0.447207383 2.151205026
[91] 0.591782352 -1.336806360 0.523272755 2.041880828 -1.233704102
[96] 0.127226816 0.705465704 -0.072668606 -0.326985798 1.083221358
> rowMin(tmp2)
[1] -0.214390412 -1.512236710 -1.424863301 -0.362960454 0.010814792
[6] -2.532576079 -0.538321826 0.513024833 0.370494186 0.256686215
[11] 1.363535717 -1.654903308 -0.290741939 1.590603096 -0.735539960
[16] -0.121696778 0.902346386 1.334482913 -0.184915290 1.590148039
[21] 1.668318969 0.637403479 0.238308353 0.919540835 -2.462816314
[26] 0.961637246 1.053173586 0.002478483 1.121295436 -0.163061618
[31] -0.023343344 -1.010626793 0.968536782 -1.516041912 -0.601715686
[36] 0.588050589 0.710272721 -1.003722184 -0.648256257 -1.191980360
[41] 1.899844905 0.198478937 -1.445815729 0.690712250 -0.436857020
[46] -0.534486386 -0.313324758 -0.276687003 1.023069794 -1.411752763
[51] -0.331678662 0.774125053 -0.223915972 0.998837483 0.941045306
[56] 1.516789997 -2.740722269 -1.182181952 0.340606388 -0.653233326
[61] 1.125131937 1.597410034 0.184672134 1.961180314 -1.795675006
[66] 2.531138430 0.458771373 -0.309086264 -0.633556120 -0.805153894
[71] -0.349900686 0.620750298 -1.585876391 0.991386635 0.926005372
[76] 1.185653376 0.584261130 -0.977868026 0.415175066 -2.434317889
[81] -1.633886555 -0.159227845 0.801936819 2.233942568 1.359429992
[86] -0.779266166 -0.689622846 -0.504849076 0.447207383 2.151205026
[91] 0.591782352 -1.336806360 0.523272755 2.041880828 -1.233704102
[96] 0.127226816 0.705465704 -0.072668606 -0.326985798 1.083221358
>
> colMeans(tmp2)
[1] 0.06458952
> colSums(tmp2)
[1] 6.458952
> colVars(tmp2)
[1] 1.301657
> colSd(tmp2)
[1] 1.140902
> colMax(tmp2)
[1] 2.531138
> colMin(tmp2)
[1] -2.740722
> colMedians(tmp2)
[1] 0.0690208
> colRanges(tmp2)
[,1]
[1,] -2.740722
[2,] 2.531138
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.31796237 -1.89372328 2.98624683 -0.45987072 -6.67905011 -2.04506225
[7] -4.40056598 0.08790962 -2.72502979 0.17505394
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.70253377
[2,] -0.36837564
[3,] 0.07941861
[4,] 0.76822091
[5,] 1.69840935
>
> rowApply(tmp,sum)
[1] -5.509181 -1.977837 2.160243 -1.234055 1.156295 -2.759908 -2.470284
[8] -0.192027 -5.345590 3.536216
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 6 1 10 10 9 5 2 8 5
[2,] 2 4 7 1 9 6 3 10 4 9
[3,] 10 7 2 8 4 8 4 6 6 10
[4,] 5 10 8 7 1 10 9 1 1 3
[5,] 1 1 6 9 3 5 2 4 3 6
[6,] 7 3 3 2 5 7 1 5 10 1
[7,] 4 5 10 6 2 1 8 3 2 4
[8,] 3 9 9 4 8 3 6 9 9 7
[9,] 6 2 5 3 7 4 10 7 7 2
[10,] 8 8 4 5 6 2 7 8 5 8
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.3513295 -2.9363840 -2.4630684 -7.1480672 1.0535714 1.1891460
[7] 4.5913560 -2.5378130 4.1292379 -2.8475124 2.2122180 -3.7115801
[13] -1.4656888 -0.0322784 2.2470670 -5.9876741 0.0284314 5.1273082
[19] -1.3662014 -5.9481902
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.7840027
[2,] -1.5966219
[3,] -1.0967513
[4,] 0.4977646
[5,] 1.6282819
>
> rowApply(tmp,sum)
[1] -5.0547269 -8.0086169 -0.4664562 -7.2048168 2.5171655
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 4 5 18 3 11
[2,] 6 10 2 13 9
[3,] 9 16 1 8 18
[4,] 2 7 4 1 8
[5,] 17 14 13 7 12
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.7840027 -0.92095188 -0.6627532 -1.8527090 1.1159215 -0.78342763
[2,] -1.0967513 -0.31936833 0.5266930 -0.7377204 0.2116961 0.60015619
[3,] 1.6282819 -1.59470035 -2.4842301 -1.5395931 0.3439434 0.05079772
[4,] -1.5966219 -0.07497272 -1.1421622 -2.8619424 -1.2655424 0.23843497
[5,] 0.4977646 -0.02639068 1.2993840 -0.1561022 0.6475529 1.08318477
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 2.6624383 -0.3709838 1.8929053 -0.307585148 -0.1865654 -1.9268166
[2,] -0.5506425 -0.5540126 -2.6290956 0.001220095 0.8892852 -0.3135967
[3,] 1.1730022 -0.3252714 2.5058796 0.227438803 -0.0404739 -0.9179765
[4,] 1.4694851 -0.4410332 3.0298192 -0.090268291 0.8833434 -1.4786306
[5,] -0.1629271 -0.8465120 -0.6702705 -2.678317836 0.6666287 0.9254402
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.03363173 1.4732093 0.9116430 -1.7395689 -0.10611421 -0.9054159
[2,] 0.79517007 -0.7571862 0.2586415 -1.6851647 -1.23850945 0.5991514
[3,] -1.05710861 -1.5587548 -0.4785864 -0.5413767 0.55203206 2.2679633
[4,] 0.79520330 -1.4518772 -1.0902022 -0.8582010 0.05220271 2.3150773
[5,] -2.03258524 2.2623305 2.6455712 -1.1633628 0.76882029 0.8505322
[,19] [,20]
[1,] 0.21791109 -1.8154927
[2,] -0.04470686 -1.9638757
[3,] 0.48655807 0.8357185
[4,] -2.04478224 -1.5921463
[5,] 0.01881856 -1.4123941
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 631 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 547 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -1.085371 -1.260768 0.9573885 -0.8582618 0.01509585 0.05106094 -2.323768
col8 col9 col10 col11 col12 col13 col14
row1 0.3850234 0.8025808 0.8709114 -0.7581347 -0.2576377 0.4814554 -0.1200233
col15 col16 col17 col18 col19 col20
row1 -1.122997 -0.6380345 -0.4578275 -0.5133622 -0.6245459 0.4174373
> tmp[,"col10"]
col10
row1 0.87091140
row2 1.97753051
row3 -0.01094557
row4 -0.22653104
row5 0.44894299
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -1.0853715 -1.26076824 0.9573885 -0.8582618 0.01509585 0.05106094
row5 0.8571507 -0.02551664 0.6941146 1.9899278 -0.62524380 -0.58456197
col7 col8 col9 col10 col11 col12
row1 -2.323768 0.3850234 0.8025808 0.8709114 -0.7581347 -0.25763772
row5 1.131616 -0.1161122 0.1208820 0.4489430 0.8980931 -0.05163723
col13 col14 col15 col16 col17 col18
row1 0.48145538 -0.1200233 -1.122997 -0.6380345 -0.4578275 -0.51336216
row5 -0.08882013 0.8800396 -1.193233 0.1362215 0.4293721 -0.05315136
col19 col20
row1 -0.6245459 0.4174373
row5 -0.1384584 0.9541303
> tmp[,c("col6","col20")]
col6 col20
row1 0.05106094 0.4174373
row2 -1.17691750 -0.9917544
row3 0.67054435 2.3788472
row4 0.63441614 -0.8681977
row5 -0.58456197 0.9541303
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.05106094 0.4174373
row5 -0.58456197 0.9541303
>
>
>
>
> 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 50.58536 49.53473 48.67377 49.47866 50.90695 104.5284 51.08342 49.55036
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.66674 50.0799 49.98263 49.48422 49.60555 52.19767 52.22302 49.47937
col17 col18 col19 col20
row1 48.85676 49.09393 50.44572 104.972
> tmp[,"col10"]
col10
row1 50.07990
row2 30.43892
row3 28.98649
row4 30.14424
row5 50.48622
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.58536 49.53473 48.67377 49.47866 50.90695 104.5284 51.08342 49.55036
row5 49.70291 51.16764 48.73224 49.64729 50.89258 104.9780 48.12822 49.66284
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.66674 50.07990 49.98263 49.48422 49.60555 52.19767 52.22302 49.47937
row5 48.55015 50.48622 51.93383 50.71777 50.85371 50.67657 50.55505 50.80594
col17 col18 col19 col20
row1 48.85676 49.09393 50.44572 104.9720
row5 50.06666 51.53397 50.27853 105.1919
> tmp[,c("col6","col20")]
col6 col20
row1 104.52845 104.97202
row2 73.81511 74.36222
row3 76.02129 75.77767
row4 74.90034 74.84057
row5 104.97803 105.19191
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.5284 104.9720
row5 104.9780 105.1919
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.5284 104.9720
row5 104.9780 105.1919
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.3787126
[2,] -0.6241757
[3,] -0.6575744
[4,] 1.2196913
[5,] -1.0611734
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.2993927 1.0899835
[2,] 1.3057411 0.2431684
[3,] -1.8500941 -0.4921783
[4,] -1.8684063 -0.4143306
[5,] -0.5259552 0.8480081
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.1147809 -0.01844677
[2,] 0.1325274 -0.15306051
[3,] 0.3994236 1.23929842
[4,] -0.6520889 -1.17217712
[5,] 0.4224806 0.66397282
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.1147809
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.1147809
[2,] 0.1325274
>
>
>
> 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 -0.2063024 0.1682764 0.5449885 -1.23091719 -1.210799 1.266735 1.6145111
row1 0.2484207 -1.4765071 1.3360830 0.07494366 0.685517 1.073715 0.3953541
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.9327964 1.4366488 -0.7022283 0.9060817 -0.09585533 -0.7108322
row1 0.5207707 0.6030624 0.8994105 -1.0195994 0.48200054 0.7628434
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.6793694 -1.7479075 0.2121546 0.1771213 -1.211638 -0.9146662 -1.353176
row1 0.6089346 0.2712136 0.7032921 1.1239460 -1.061838 -1.3937591 -1.441162
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.440933 -1.807047 0.4064202 -1.568598 -1.622348 -0.7892351 1.763943
[,8] [,9] [,10]
row2 1.560508 -1.011471 1.014543
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.4096525 0.07449771 1.048363 1.460242 -0.2770127 -1.482593 0.1170546
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.3794637 0.4288249 1.479878 1.081234 0.9948591 -2.186738 0.2947707
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.5140555 -1.46052 0.5059039 -0.7587213 1.406504 0.07954193
>
>
> 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: 0x000002a20faf8710>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM2306416d12679"
[2] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM23064638c2fa1"
[3] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230642b261c3a"
[4] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM2306455441fc9"
[5] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230644ffc7e0b"
[6] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230642e184cb8"
[7] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM23064c354493"
[8] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230641c2323e9"
[9] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230646feb75d7"
[10] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230642a696d21"
[11] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230642961365b"
[12] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230641d6b4af"
[13] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230646639758a"
[14] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM230647df9af2"
[15] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM2306454e73958"
>
>
> ### 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: 0x000002a2121ff410>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x000002a2121ff410>
Warning message:
In dir.create(new.directory) :
'F:\biocbuild\bbs-3.20-bioc\meat\BufferedMatrix.Rcheck\tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x000002a2121ff410>
> rowMedians(tmp)
[1] -0.057765443 -0.279197672 0.380675992 0.591447781 0.368574768
[6] -0.161422893 0.722841034 0.497787348 0.208997910 0.072945796
[11] 0.512989864 -0.437638938 -0.454686344 -0.263414046 -0.310624370
[16] -0.054415306 0.034336703 -0.575706263 -0.100240988 0.278479347
[21] 0.192236858 -0.084610289 -0.041087560 0.020343368 0.183422307
[26] 0.020389255 0.306596060 0.615859915 0.155469858 0.638700798
[31] 0.175137950 0.219610913 -0.593983029 -0.033807244 -0.419451275
[36] 0.451850664 0.151985290 -0.033949654 -0.359794080 -0.180716471
[41] -0.308029707 -0.638210677 -0.162251039 -0.445249655 -0.294356450
[46] -0.152256468 0.215279593 0.486818788 0.542982294 0.176960618
[51] 0.153467244 -0.179936474 -0.400742472 -0.012489640 -0.024204768
[56] 0.408550817 0.124633199 0.248771948 0.274403701 0.867391006
[61] -0.516752027 0.269868236 -0.096305323 -0.094139387 -0.247746531
[66] 0.021407177 -0.222549900 -0.407725288 0.016730182 -0.014649452
[71] 0.226726362 -0.642668433 0.073236776 -0.096100496 -0.264397818
[76] 0.280940723 0.145462330 -0.365729972 -0.523303268 0.068726270
[81] 0.528638261 -0.209332229 -0.136350512 -0.516403704 -0.312331498
[86] -0.058215799 -0.496056769 -0.447205150 0.195060961 -0.062482263
[91] -0.221957900 -0.133084631 -0.265260460 -0.528415522 -0.026541974
[96] 0.012041396 0.316958774 0.737998283 -0.192092654 0.444257536
[101] 0.341252369 -0.268904172 0.002574403 0.098423339 -0.484337148
[106] -0.215236684 0.120998458 -0.265391138 -0.264602494 -0.539971515
[111] 0.533096549 -0.222338685 -0.038338920 0.181217691 0.694624671
[116] -0.140751359 0.190662448 -0.207867505 -0.227781921 -0.449100655
[121] 0.211447862 0.097785562 -0.070219679 0.112754640 -0.010503326
[126] -0.304318722 -0.580605747 -0.036939142 -0.302981354 0.186358159
[131] 0.221554299 -0.059592529 0.170359041 -0.243416772 0.194951971
[136] 0.196301143 0.347663461 -0.166971674 0.232231381 -0.495863796
[141] -0.603857248 0.382235802 0.311439158 0.704725056 -0.459351246
[146] -0.619156172 -0.256785695 -0.351933399 -0.192279098 0.298362875
[151] -0.220201360 0.008623363 0.272963290 -0.498864759 0.261221405
[156] 0.293316277 -0.037385690 -0.223218694 0.017231466 0.229957934
[161] -0.345817965 0.262262642 -0.244650893 0.469233256 0.445401365
[166] 0.109791393 -0.013708830 0.102410159 -0.197070778 0.323255205
[171] -0.360621500 -0.111050732 -0.233869962 -1.080290396 0.215613416
[176] -0.098377360 0.004931737 -0.059351877 0.168979302 0.143225719
[181] -0.416308192 -0.394011773 0.389655308 0.065814866 -0.083751863
[186] 0.480420931 0.621035163 -0.028327737 0.277841610 0.097111163
[191] 0.321645267 -0.131597632 0.397038074 -0.076913732 -0.206534437
[196] -0.340591917 0.146439367 0.360211603 0.441065076 -0.298783483
[201] -0.498433619 0.019979788 -0.340299556 0.262577732 0.079898372
[206] 0.016310126 0.259524749 -0.038866661 0.032587575 0.153082376
[211] -0.124199655 -0.405874887 -0.162215820 -0.253579056 -0.229236679
[216] -0.930410195 0.413203333 0.022781399 0.164141187 -0.338855022
[221] -0.136499190 0.034041911 -0.651790495 0.783910599 0.272184469
[226] 0.030649704 0.063864176 0.151314839 0.388995921 0.172031849
>
> proc.time()
user system elapsed
4.00 14.73 143.54
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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: 0x0000020570efeb30>
> .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: 0x0000020570efeb30>
> .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: 0x0000020570efeb30>
> .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: 0x0000020570efeb30>
> 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: 0x0000020570efe290>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020570efe290>
> .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: 0x0000020570efe290>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020570efe290>
> .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: 0x0000020570efe290>
> 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: 0x0000020570efed70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020570efed70>
> .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: 0x0000020570efed70>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x0000020570efed70>
> .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: 0x0000020570efed70>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x0000020570efed70>
> .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: 0x0000020570efed70>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x0000020570efed70>
> .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: 0x0000020570efed70>
> 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: 0x0000020570efedd0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x0000020570efedd0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020570efedd0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x0000020570efedd0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1ff803321318" "BufferedMatrixFile1ff803a40620f"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1ff803321318" "BufferedMatrixFile1ff803a40620f"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000205735ff0b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000205735ff0b0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000205735ff0b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000205735ff0b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x00000205735ff0b0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x00000205735ff0b0>
> .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: 0x00000205735ff5f0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000205735ff5f0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000205735ff5f0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x00000205735ff5f0>
> 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: 0x00000205735ff230>
> .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: 0x00000205735ff230>
> rm(P)
>
> proc.time()
user system elapsed
0.26 0.14 0.64
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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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
0.34 0.10 0.39