Ben Bolstad
| Snapshot Date: 2026-01-15 13:40 -0500 (Thu, 15 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: ecdbf23 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-16 11:11 -0500 (Fri, 16 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4849 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4628 |
| 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 253/2343 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.75.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2026-01-15 21:51:59 -0500 (Thu, 15 Jan 2026) |
| EndedAt: 2026-01-15 21:52:24 -0500 (Thu, 15 Jan 2026) |
| EllapsedTime: 25.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.75.0’
* 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 ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 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 loading without being on the library search path ... 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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 Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
0.258 0.047 0.294
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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] "/home/biocbuild/bbs-3.23-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 478851 25.6 1048487 56 639317 34.2
Vcells 885659 6.8 8388608 64 2082734 15.9
>
>
>
>
> ##
> ## 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 Jan 15 21:52:15 2026"
> 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 Jan 15 21:52:15 2026"
>
>
> 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: 0x5f1d648082b0>
>
>
>
> 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 Jan 15 21:52:15 2026"
> 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 Jan 15 21:52:15 2026"
>
> ColMode(tmp2)
<pointer: 0x5f1d648082b0>
>
>
>
> ### 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,] 99.170618094 -1.6699608 -0.4986535 1.3283884
[2,] -0.148110196 1.9410338 -1.8288647 0.3296034
[3,] -0.475480414 -0.1788284 0.8889732 0.6339862
[4,] -0.008737906 2.8781920 3.4547139 -0.5723434
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.170618094 1.6699608 0.4986535 1.3283884
[2,] 0.148110196 1.9410338 1.8288647 0.3296034
[3,] 0.475480414 0.1788284 0.8889732 0.6339862
[4,] 0.008737906 2.8781920 3.4547139 0.5723434
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.95844456 1.292270 0.7061540 1.1525573
[2,] 0.38485088 1.393210 1.3523552 0.5741110
[3,] 0.68955088 0.422881 0.9428538 0.7962325
[4,] 0.09347677 1.696524 1.8586861 0.7565338
>
> 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: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 223.75506 39.59266 32.56019 37.85396
[2,] 28.99662 40.87313 40.35242 31.07071
[3,] 32.37099 29.40764 35.31751 33.59631
[4,] 25.94351 44.84343 47.04157 33.13768
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5f1d64f0f500>
> exp(tmp5)
<pointer: 0x5f1d64f0f500>
> log(tmp5,2)
<pointer: 0x5f1d64f0f500>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 465.7168
> Min(tmp5)
[1] 52.97899
> mean(tmp5)
[1] 73.10064
> Sum(tmp5)
[1] 14620.13
> Var(tmp5)
[1] 856.7302
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.15760 70.52246 68.43460 70.72574 69.35900 74.52175 73.85849 71.35294
[9] 71.55065 68.52318
> rowSums(tmp5)
[1] 1843.152 1410.449 1368.692 1414.515 1387.180 1490.435 1477.170 1427.059
[9] 1431.013 1370.464
> rowVars(tmp5)
[1] 7815.46458 98.91541 56.73361 133.68093 76.63880 50.21503
[7] 97.61173 59.34886 48.53913 72.57261
> rowSd(tmp5)
[1] 88.405116 9.945623 7.532172 11.562047 8.754359 7.086257 9.879865
[8] 7.703821 6.967003 8.518956
> rowMax(tmp5)
[1] 465.71685 89.27951 81.02604 97.91087 85.66849 84.39957 91.58084
[8] 85.82557 87.92001 92.55115
> rowMin(tmp5)
[1] 55.11813 55.30886 55.71527 53.99801 52.97899 61.64049 53.40392 58.66537
[9] 60.49533 56.85895
>
> colMeans(tmp5)
[1] 107.74795 74.34391 76.01017 72.03378 71.81926 66.04199 66.88058
[8] 69.75086 74.96076 74.48576 73.98872 71.37314 70.55866 69.85478
[15] 70.76088 70.64615 69.27178 72.59428 67.51158 71.37784
> colSums(tmp5)
[1] 1077.4795 743.4391 760.1017 720.3378 718.1926 660.4199 668.8058
[8] 697.5086 749.6076 744.8576 739.8872 713.7314 705.5866 698.5478
[15] 707.6088 706.4615 692.7178 725.9428 675.1158 713.7784
> colVars(tmp5)
[1] 15921.03951 121.50787 100.66308 99.27262 58.34090 80.77716
[7] 67.37880 103.82369 93.42736 95.17626 57.73823 45.73318
[13] 116.94406 122.57307 49.17901 44.90270 52.45468 34.24187
[19] 42.71320 80.11091
> colSd(tmp5)
[1] 126.178602 11.023061 10.033099 9.963565 7.638121 8.987612
[7] 8.208459 10.189391 9.665783 9.755832 7.598568 6.762631
[13] 10.814068 11.071272 7.012775 6.700948 7.242560 5.851655
[19] 6.535534 8.950470
> colMax(tmp5)
[1] 465.71685 93.33572 97.91087 87.92001 82.24235 82.42719 79.33314
[8] 88.65397 91.58084 88.77542 85.66849 82.32567 89.27951 92.55115
[15] 80.95798 79.87485 84.36779 81.02604 79.46001 84.68761
> colMin(tmp5)
[1] 53.99801 61.20815 62.21984 56.21091 58.21794 53.40392 55.30886 56.83079
[9] 54.91585 52.97899 62.52982 63.65494 55.11813 55.83330 60.24040 57.19605
[17] 60.46428 64.28291 56.85895 55.96188
>
>
> ### 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] 92.15760 70.52246 68.43460 70.72574 NA 74.52175 73.85849 71.35294
[9] 71.55065 68.52318
> rowSums(tmp5)
[1] 1843.152 1410.449 1368.692 1414.515 NA 1490.435 1477.170 1427.059
[9] 1431.013 1370.464
> rowVars(tmp5)
[1] 7815.46458 98.91541 56.73361 133.68093 77.97596 50.21503
[7] 97.61173 59.34886 48.53913 72.57261
> rowSd(tmp5)
[1] 88.405116 9.945623 7.532172 11.562047 8.830400 7.086257 9.879865
[8] 7.703821 6.967003 8.518956
> rowMax(tmp5)
[1] 465.71685 89.27951 81.02604 97.91087 NA 84.39957 91.58084
[8] 85.82557 87.92001 92.55115
> rowMin(tmp5)
[1] 55.11813 55.30886 55.71527 53.99801 NA 61.64049 53.40392 58.66537
[9] 60.49533 56.85895
>
> colMeans(tmp5)
[1] 107.74795 74.34391 76.01017 72.03378 71.81926 66.04199 66.88058
[8] NA 74.96076 74.48576 73.98872 71.37314 70.55866 69.85478
[15] 70.76088 70.64615 69.27178 72.59428 67.51158 71.37784
> colSums(tmp5)
[1] 1077.4795 743.4391 760.1017 720.3378 718.1926 660.4199 668.8058
[8] NA 749.6076 744.8576 739.8872 713.7314 705.5866 698.5478
[15] 707.6088 706.4615 692.7178 725.9428 675.1158 713.7784
> colVars(tmp5)
[1] 15921.03951 121.50787 100.66308 99.27262 58.34090 80.77716
[7] 67.37880 NA 93.42736 95.17626 57.73823 45.73318
[13] 116.94406 122.57307 49.17901 44.90270 52.45468 34.24187
[19] 42.71320 80.11091
> colSd(tmp5)
[1] 126.178602 11.023061 10.033099 9.963565 7.638121 8.987612
[7] 8.208459 NA 9.665783 9.755832 7.598568 6.762631
[13] 10.814068 11.071272 7.012775 6.700948 7.242560 5.851655
[19] 6.535534 8.950470
> colMax(tmp5)
[1] 465.71685 93.33572 97.91087 87.92001 82.24235 82.42719 79.33314
[8] NA 91.58084 88.77542 85.66849 82.32567 89.27951 92.55115
[15] 80.95798 79.87485 84.36779 81.02604 79.46001 84.68761
> colMin(tmp5)
[1] 53.99801 61.20815 62.21984 56.21091 58.21794 53.40392 55.30886 NA
[9] 54.91585 52.97899 62.52982 63.65494 55.11813 55.83330 60.24040 57.19605
[17] 60.46428 64.28291 56.85895 55.96188
>
> Max(tmp5,na.rm=TRUE)
[1] 465.7168
> Min(tmp5,na.rm=TRUE)
[1] 52.97899
> mean(tmp5,na.rm=TRUE)
[1] 73.08393
> Sum(tmp5,na.rm=TRUE)
[1] 14543.7
> Var(tmp5,na.rm=TRUE)
[1] 861.001
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.15760 70.52246 68.43460 70.72574 68.98706 74.52175 73.85849 71.35294
[9] 71.55065 68.52318
> rowSums(tmp5,na.rm=TRUE)
[1] 1843.152 1410.449 1368.692 1414.515 1310.754 1490.435 1477.170 1427.059
[9] 1431.013 1370.464
> rowVars(tmp5,na.rm=TRUE)
[1] 7815.46458 98.91541 56.73361 133.68093 77.97596 50.21503
[7] 97.61173 59.34886 48.53913 72.57261
> rowSd(tmp5,na.rm=TRUE)
[1] 88.405116 9.945623 7.532172 11.562047 8.830400 7.086257 9.879865
[8] 7.703821 6.967003 8.518956
> rowMax(tmp5,na.rm=TRUE)
[1] 465.71685 89.27951 81.02604 97.91087 85.66849 84.39957 91.58084
[8] 85.82557 87.92001 92.55115
> rowMin(tmp5,na.rm=TRUE)
[1] 55.11813 55.30886 55.71527 53.99801 52.97899 61.64049 53.40392 58.66537
[9] 60.49533 56.85895
>
> colMeans(tmp5,na.rm=TRUE)
[1] 107.74795 74.34391 76.01017 72.03378 71.81926 66.04199 66.88058
[8] 69.00919 74.96076 74.48576 73.98872 71.37314 70.55866 69.85478
[15] 70.76088 70.64615 69.27178 72.59428 67.51158 71.37784
> colSums(tmp5,na.rm=TRUE)
[1] 1077.4795 743.4391 760.1017 720.3378 718.1926 660.4199 668.8058
[8] 621.0827 749.6076 744.8576 739.8872 713.7314 705.5866 698.5478
[15] 707.6088 706.4615 692.7178 725.9428 675.1158 713.7784
> colVars(tmp5,na.rm=TRUE)
[1] 15921.03951 121.50787 100.66308 99.27262 58.34090 80.77716
[7] 67.37880 110.61327 93.42736 95.17626 57.73823 45.73318
[13] 116.94406 122.57307 49.17901 44.90270 52.45468 34.24187
[19] 42.71320 80.11091
> colSd(tmp5,na.rm=TRUE)
[1] 126.178602 11.023061 10.033099 9.963565 7.638121 8.987612
[7] 8.208459 10.517284 9.665783 9.755832 7.598568 6.762631
[13] 10.814068 11.071272 7.012775 6.700948 7.242560 5.851655
[19] 6.535534 8.950470
> colMax(tmp5,na.rm=TRUE)
[1] 465.71685 93.33572 97.91087 87.92001 82.24235 82.42719 79.33314
[8] 88.65397 91.58084 88.77542 85.66849 82.32567 89.27951 92.55115
[15] 80.95798 79.87485 84.36779 81.02604 79.46001 84.68761
> colMin(tmp5,na.rm=TRUE)
[1] 53.99801 61.20815 62.21984 56.21091 58.21794 53.40392 55.30886 56.83079
[9] 54.91585 52.97899 62.52982 63.65494 55.11813 55.83330 60.24040 57.19605
[17] 60.46428 64.28291 56.85895 55.96188
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.15760 70.52246 68.43460 70.72574 NaN 74.52175 73.85849 71.35294
[9] 71.55065 68.52318
> rowSums(tmp5,na.rm=TRUE)
[1] 1843.152 1410.449 1368.692 1414.515 0.000 1490.435 1477.170 1427.059
[9] 1431.013 1370.464
> rowVars(tmp5,na.rm=TRUE)
[1] 7815.46458 98.91541 56.73361 133.68093 NA 50.21503
[7] 97.61173 59.34886 48.53913 72.57261
> rowSd(tmp5,na.rm=TRUE)
[1] 88.405116 9.945623 7.532172 11.562047 NA 7.086257 9.879865
[8] 7.703821 6.967003 8.518956
> rowMax(tmp5,na.rm=TRUE)
[1] 465.71685 89.27951 81.02604 97.91087 NA 84.39957 91.58084
[8] 85.82557 87.92001 92.55115
> rowMin(tmp5,na.rm=TRUE)
[1] 55.11813 55.30886 55.71527 53.99801 NA 61.64049 53.40392 58.66537
[9] 60.49533 56.85895
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 111.80770 75.14632 76.87953 73.79187 71.44253 66.74681 66.41870
[8] NaN 74.38504 76.87540 72.69097 72.23072 71.11256 71.33756
[15] 69.78940 70.19315 69.05147 73.50273 67.24742 70.66850
> colSums(tmp5,na.rm=TRUE)
[1] 1006.2693 676.3169 691.9158 664.1268 642.9828 600.7213 597.7683
[8] 0.0000 669.4654 691.8786 654.2187 650.0765 640.0130 642.0380
[15] 628.1046 631.7384 621.4632 661.5246 605.2268 636.0165
> colVars(tmp5,na.rm=TRUE)
[1] 17725.75158 129.45288 104.74333 76.90907 64.03689 85.28552
[7] 73.40113 NA 101.37695 42.83146 46.00870 43.17614
[13] 128.11053 113.16002 44.70888 48.20702 58.46546 29.23774
[19] 47.26731 84.46420
> colSd(tmp5,na.rm=TRUE)
[1] 133.138092 11.377736 10.234419 8.769782 8.002305 9.235016
[7] 8.567446 NA 10.068612 6.544575 6.782971 6.570855
[13] 11.318592 10.637670 6.686470 6.943128 7.646271 5.407193
[19] 6.875122 9.190441
> colMax(tmp5,na.rm=TRUE)
[1] 465.71685 93.33572 97.91087 87.92001 82.24235 82.42719 79.33314
[8] -Inf 91.58084 88.77542 80.37830 82.32567 89.27951 92.55115
[15] 80.95798 79.87485 84.36779 81.02604 79.46001 84.68761
> colMin(tmp5,na.rm=TRUE)
[1] 53.99801 61.20815 62.21984 61.27745 58.21794 53.40392 55.30886 Inf
[9] 54.91585 67.87645 62.52982 65.13498 55.11813 55.83330 60.24040 57.19605
[17] 60.46428 64.28291 56.85895 55.96188
>
>
>
>
> 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] 205.5792 105.1537 234.5121 192.8290 245.6195 193.3858 172.9146 247.2585
[9] 172.2694 136.7806
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 205.5792 105.1537 234.5121 192.8290 245.6195 193.3858 172.9146 247.2585
[9] 172.2694 136.7806
>
>
>
> 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 2.842171e-14 -5.684342e-14 -1.136868e-13 2.842171e-14
[6] 8.526513e-14 -8.526513e-14 2.842171e-14 -8.526513e-14 0.000000e+00
[11] 1.278977e-13 -2.273737e-13 9.947598e-14 -1.421085e-13 -2.273737e-13
[16] 1.705303e-13 -5.684342e-14 0.000000e+00 -5.684342e-14 -1.705303e-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)
+ }
9 10
6 17
10 18
2 2
1 3
2 17
4 8
10 9
4 13
3 10
1 11
10 17
3 4
7 9
4 6
7 19
10 1
1 4
6 10
5 6
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] 2.620908
> Min(tmp)
[1] -2.711411
> mean(tmp)
[1] 0.00893978
> Sum(tmp)
[1] 0.893978
> Var(tmp)
[1] 1.318157
>
> rowMeans(tmp)
[1] 0.00893978
> rowSums(tmp)
[1] 0.893978
> rowVars(tmp)
[1] 1.318157
> rowSd(tmp)
[1] 1.14811
> rowMax(tmp)
[1] 2.620908
> rowMin(tmp)
[1] -2.711411
>
> colMeans(tmp)
[1] -0.51619574 -0.36339326 -0.37900726 1.31202700 -2.37769284 0.08742994
[7] 1.12954752 -1.04150886 -0.04785266 0.60198318 0.87044858 -1.65938761
[13] 1.81260767 -1.88512922 2.62090812 -0.50848687 -0.03557204 -0.96151065
[19] 1.18717937 -2.61843477 -0.12499886 -0.61272846 -0.37467261 1.30765011
[25] -1.64183268 0.21146641 0.33308051 -0.27166274 1.37238926 -0.93330718
[31] 0.06354339 0.19841855 0.13910901 0.53005046 -0.99336674 0.64316738
[37] -1.89360418 -0.43822115 1.20829105 -0.45466214 0.16593249 -0.46384621
[43] -0.36383663 -1.24765795 0.44515588 0.20356401 -1.50573617 0.06930986
[49] 0.09026001 -0.09310484 2.27567819 0.99959494 -0.93006475 0.67982039
[55] 0.51106653 -1.91636221 -1.92670573 -0.17051397 -2.71141063 0.04607177
[61] 1.05364800 -0.51732627 -1.27232238 1.40320415 0.68805372 1.07181823
[67] -0.58868696 1.30125359 2.14415789 1.87588488 -1.28333261 -1.36467602
[73] 0.05377782 1.09134357 0.62795587 2.43960682 1.28617023 0.92866035
[79] -0.21509886 0.33604676 0.35812797 1.87176931 -0.46252234 0.63396059
[85] -1.53384931 0.48519896 0.72408653 1.01484744 -0.77384178 -0.10586449
[91] -2.05233762 -1.92244613 -0.22222908 -0.36622229 -0.65149985 0.35843667
[97] 0.84592154 1.20375732 0.88960818 -0.11434639
> colSums(tmp)
[1] -0.51619574 -0.36339326 -0.37900726 1.31202700 -2.37769284 0.08742994
[7] 1.12954752 -1.04150886 -0.04785266 0.60198318 0.87044858 -1.65938761
[13] 1.81260767 -1.88512922 2.62090812 -0.50848687 -0.03557204 -0.96151065
[19] 1.18717937 -2.61843477 -0.12499886 -0.61272846 -0.37467261 1.30765011
[25] -1.64183268 0.21146641 0.33308051 -0.27166274 1.37238926 -0.93330718
[31] 0.06354339 0.19841855 0.13910901 0.53005046 -0.99336674 0.64316738
[37] -1.89360418 -0.43822115 1.20829105 -0.45466214 0.16593249 -0.46384621
[43] -0.36383663 -1.24765795 0.44515588 0.20356401 -1.50573617 0.06930986
[49] 0.09026001 -0.09310484 2.27567819 0.99959494 -0.93006475 0.67982039
[55] 0.51106653 -1.91636221 -1.92670573 -0.17051397 -2.71141063 0.04607177
[61] 1.05364800 -0.51732627 -1.27232238 1.40320415 0.68805372 1.07181823
[67] -0.58868696 1.30125359 2.14415789 1.87588488 -1.28333261 -1.36467602
[73] 0.05377782 1.09134357 0.62795587 2.43960682 1.28617023 0.92866035
[79] -0.21509886 0.33604676 0.35812797 1.87176931 -0.46252234 0.63396059
[85] -1.53384931 0.48519896 0.72408653 1.01484744 -0.77384178 -0.10586449
[91] -2.05233762 -1.92244613 -0.22222908 -0.36622229 -0.65149985 0.35843667
[97] 0.84592154 1.20375732 0.88960818 -0.11434639
> 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] -0.51619574 -0.36339326 -0.37900726 1.31202700 -2.37769284 0.08742994
[7] 1.12954752 -1.04150886 -0.04785266 0.60198318 0.87044858 -1.65938761
[13] 1.81260767 -1.88512922 2.62090812 -0.50848687 -0.03557204 -0.96151065
[19] 1.18717937 -2.61843477 -0.12499886 -0.61272846 -0.37467261 1.30765011
[25] -1.64183268 0.21146641 0.33308051 -0.27166274 1.37238926 -0.93330718
[31] 0.06354339 0.19841855 0.13910901 0.53005046 -0.99336674 0.64316738
[37] -1.89360418 -0.43822115 1.20829105 -0.45466214 0.16593249 -0.46384621
[43] -0.36383663 -1.24765795 0.44515588 0.20356401 -1.50573617 0.06930986
[49] 0.09026001 -0.09310484 2.27567819 0.99959494 -0.93006475 0.67982039
[55] 0.51106653 -1.91636221 -1.92670573 -0.17051397 -2.71141063 0.04607177
[61] 1.05364800 -0.51732627 -1.27232238 1.40320415 0.68805372 1.07181823
[67] -0.58868696 1.30125359 2.14415789 1.87588488 -1.28333261 -1.36467602
[73] 0.05377782 1.09134357 0.62795587 2.43960682 1.28617023 0.92866035
[79] -0.21509886 0.33604676 0.35812797 1.87176931 -0.46252234 0.63396059
[85] -1.53384931 0.48519896 0.72408653 1.01484744 -0.77384178 -0.10586449
[91] -2.05233762 -1.92244613 -0.22222908 -0.36622229 -0.65149985 0.35843667
[97] 0.84592154 1.20375732 0.88960818 -0.11434639
> colMin(tmp)
[1] -0.51619574 -0.36339326 -0.37900726 1.31202700 -2.37769284 0.08742994
[7] 1.12954752 -1.04150886 -0.04785266 0.60198318 0.87044858 -1.65938761
[13] 1.81260767 -1.88512922 2.62090812 -0.50848687 -0.03557204 -0.96151065
[19] 1.18717937 -2.61843477 -0.12499886 -0.61272846 -0.37467261 1.30765011
[25] -1.64183268 0.21146641 0.33308051 -0.27166274 1.37238926 -0.93330718
[31] 0.06354339 0.19841855 0.13910901 0.53005046 -0.99336674 0.64316738
[37] -1.89360418 -0.43822115 1.20829105 -0.45466214 0.16593249 -0.46384621
[43] -0.36383663 -1.24765795 0.44515588 0.20356401 -1.50573617 0.06930986
[49] 0.09026001 -0.09310484 2.27567819 0.99959494 -0.93006475 0.67982039
[55] 0.51106653 -1.91636221 -1.92670573 -0.17051397 -2.71141063 0.04607177
[61] 1.05364800 -0.51732627 -1.27232238 1.40320415 0.68805372 1.07181823
[67] -0.58868696 1.30125359 2.14415789 1.87588488 -1.28333261 -1.36467602
[73] 0.05377782 1.09134357 0.62795587 2.43960682 1.28617023 0.92866035
[79] -0.21509886 0.33604676 0.35812797 1.87176931 -0.46252234 0.63396059
[85] -1.53384931 0.48519896 0.72408653 1.01484744 -0.77384178 -0.10586449
[91] -2.05233762 -1.92244613 -0.22222908 -0.36622229 -0.65149985 0.35843667
[97] 0.84592154 1.20375732 0.88960818 -0.11434639
> colMedians(tmp)
[1] -0.51619574 -0.36339326 -0.37900726 1.31202700 -2.37769284 0.08742994
[7] 1.12954752 -1.04150886 -0.04785266 0.60198318 0.87044858 -1.65938761
[13] 1.81260767 -1.88512922 2.62090812 -0.50848687 -0.03557204 -0.96151065
[19] 1.18717937 -2.61843477 -0.12499886 -0.61272846 -0.37467261 1.30765011
[25] -1.64183268 0.21146641 0.33308051 -0.27166274 1.37238926 -0.93330718
[31] 0.06354339 0.19841855 0.13910901 0.53005046 -0.99336674 0.64316738
[37] -1.89360418 -0.43822115 1.20829105 -0.45466214 0.16593249 -0.46384621
[43] -0.36383663 -1.24765795 0.44515588 0.20356401 -1.50573617 0.06930986
[49] 0.09026001 -0.09310484 2.27567819 0.99959494 -0.93006475 0.67982039
[55] 0.51106653 -1.91636221 -1.92670573 -0.17051397 -2.71141063 0.04607177
[61] 1.05364800 -0.51732627 -1.27232238 1.40320415 0.68805372 1.07181823
[67] -0.58868696 1.30125359 2.14415789 1.87588488 -1.28333261 -1.36467602
[73] 0.05377782 1.09134357 0.62795587 2.43960682 1.28617023 0.92866035
[79] -0.21509886 0.33604676 0.35812797 1.87176931 -0.46252234 0.63396059
[85] -1.53384931 0.48519896 0.72408653 1.01484744 -0.77384178 -0.10586449
[91] -2.05233762 -1.92244613 -0.22222908 -0.36622229 -0.65149985 0.35843667
[97] 0.84592154 1.20375732 0.88960818 -0.11434639
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.5161957 -0.3633933 -0.3790073 1.312027 -2.377693 0.08742994 1.129548
[2,] -0.5161957 -0.3633933 -0.3790073 1.312027 -2.377693 0.08742994 1.129548
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.041509 -0.04785266 0.6019832 0.8704486 -1.659388 1.812608 -1.885129
[2,] -1.041509 -0.04785266 0.6019832 0.8704486 -1.659388 1.812608 -1.885129
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 2.620908 -0.5084869 -0.03557204 -0.9615107 1.187179 -2.618435 -0.1249989
[2,] 2.620908 -0.5084869 -0.03557204 -0.9615107 1.187179 -2.618435 -0.1249989
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.6127285 -0.3746726 1.30765 -1.641833 0.2114664 0.3330805 -0.2716627
[2,] -0.6127285 -0.3746726 1.30765 -1.641833 0.2114664 0.3330805 -0.2716627
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.372389 -0.9333072 0.06354339 0.1984186 0.139109 0.5300505 -0.9933667
[2,] 1.372389 -0.9333072 0.06354339 0.1984186 0.139109 0.5300505 -0.9933667
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.6431674 -1.893604 -0.4382212 1.208291 -0.4546621 0.1659325 -0.4638462
[2,] 0.6431674 -1.893604 -0.4382212 1.208291 -0.4546621 0.1659325 -0.4638462
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.3638366 -1.247658 0.4451559 0.203564 -1.505736 0.06930986 0.09026001
[2,] -0.3638366 -1.247658 0.4451559 0.203564 -1.505736 0.06930986 0.09026001
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.09310484 2.275678 0.9995949 -0.9300648 0.6798204 0.5110665 -1.916362
[2,] -0.09310484 2.275678 0.9995949 -0.9300648 0.6798204 0.5110665 -1.916362
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.926706 -0.170514 -2.711411 0.04607177 1.053648 -0.5173263 -1.272322
[2,] -1.926706 -0.170514 -2.711411 0.04607177 1.053648 -0.5173263 -1.272322
[,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] 1.403204 0.6880537 1.071818 -0.588687 1.301254 2.144158 1.875885 -1.283333
[2,] 1.403204 0.6880537 1.071818 -0.588687 1.301254 2.144158 1.875885 -1.283333
[,72] [,73] [,74] [,75] [,76] [,77] [,78]
[1,] -1.364676 0.05377782 1.091344 0.6279559 2.439607 1.28617 0.9286603
[2,] -1.364676 0.05377782 1.091344 0.6279559 2.439607 1.28617 0.9286603
[,79] [,80] [,81] [,82] [,83] [,84] [,85]
[1,] -0.2150989 0.3360468 0.358128 1.871769 -0.4625223 0.6339606 -1.533849
[2,] -0.2150989 0.3360468 0.358128 1.871769 -0.4625223 0.6339606 -1.533849
[,86] [,87] [,88] [,89] [,90] [,91] [,92]
[1,] 0.485199 0.7240865 1.014847 -0.7738418 -0.1058645 -2.052338 -1.922446
[2,] 0.485199 0.7240865 1.014847 -0.7738418 -0.1058645 -2.052338 -1.922446
[,93] [,94] [,95] [,96] [,97] [,98] [,99]
[1,] -0.2222291 -0.3662223 -0.6514998 0.3584367 0.8459215 1.203757 0.8896082
[2,] -0.2222291 -0.3662223 -0.6514998 0.3584367 0.8459215 1.203757 0.8896082
[,100]
[1,] -0.1143464
[2,] -0.1143464
>
>
> Max(tmp2)
[1] 2.411147
> Min(tmp2)
[1] -2.466704
> mean(tmp2)
[1] -0.0754629
> Sum(tmp2)
[1] -7.54629
> Var(tmp2)
[1] 1.068415
>
> rowMeans(tmp2)
[1] -1.48448203 0.07990351 -1.22486474 0.49858768 0.62046660 0.43250490
[7] -0.99758437 0.75626948 0.32817090 -0.38059475 -1.16364295 -1.04980907
[13] 0.18961877 0.09129711 -0.41112573 0.07150415 0.28665540 1.35457321
[19] -0.64136440 -0.65126405 -0.49474314 1.76549197 2.04426852 -1.42354579
[25] 0.49204368 -1.28497965 1.54480805 1.29003638 -0.19163392 1.42787104
[31] 1.07023291 -0.91132308 -0.72773537 -1.85643042 0.02770917 -0.02253521
[37] -0.16904133 -1.34240903 -0.37637487 0.90329485 1.18283909 1.53360363
[43] 0.50609803 1.54146391 1.02757716 1.15943044 -2.46670372 0.57867402
[49] -0.19692680 -0.59351776 -0.44118895 -0.72432371 -1.96264170 -0.18690945
[55] 0.03642977 -1.93344204 1.34813094 1.79606423 -1.29512118 0.04493397
[61] 2.41114727 -1.39028680 -0.49672568 1.64362819 -0.82195892 -0.33640821
[67] 0.53321650 0.59767851 -0.87160498 -1.40432558 0.65082746 -0.06482052
[73] -1.03557179 -1.62790325 -0.01638941 0.99199181 1.29900256 0.67624165
[79] -0.02311490 1.03597807 -1.58690180 -0.37530741 0.20181335 0.43527974
[85] -1.19443859 -0.60130831 0.32649053 -0.69237298 -1.23884451 -0.79762439
[91] -0.28562769 0.21504201 -0.43385152 0.94868641 -1.42279879 -0.52607559
[97] -0.96374520 0.78727015 -0.16110700 -1.35576439
> rowSums(tmp2)
[1] -1.48448203 0.07990351 -1.22486474 0.49858768 0.62046660 0.43250490
[7] -0.99758437 0.75626948 0.32817090 -0.38059475 -1.16364295 -1.04980907
[13] 0.18961877 0.09129711 -0.41112573 0.07150415 0.28665540 1.35457321
[19] -0.64136440 -0.65126405 -0.49474314 1.76549197 2.04426852 -1.42354579
[25] 0.49204368 -1.28497965 1.54480805 1.29003638 -0.19163392 1.42787104
[31] 1.07023291 -0.91132308 -0.72773537 -1.85643042 0.02770917 -0.02253521
[37] -0.16904133 -1.34240903 -0.37637487 0.90329485 1.18283909 1.53360363
[43] 0.50609803 1.54146391 1.02757716 1.15943044 -2.46670372 0.57867402
[49] -0.19692680 -0.59351776 -0.44118895 -0.72432371 -1.96264170 -0.18690945
[55] 0.03642977 -1.93344204 1.34813094 1.79606423 -1.29512118 0.04493397
[61] 2.41114727 -1.39028680 -0.49672568 1.64362819 -0.82195892 -0.33640821
[67] 0.53321650 0.59767851 -0.87160498 -1.40432558 0.65082746 -0.06482052
[73] -1.03557179 -1.62790325 -0.01638941 0.99199181 1.29900256 0.67624165
[79] -0.02311490 1.03597807 -1.58690180 -0.37530741 0.20181335 0.43527974
[85] -1.19443859 -0.60130831 0.32649053 -0.69237298 -1.23884451 -0.79762439
[91] -0.28562769 0.21504201 -0.43385152 0.94868641 -1.42279879 -0.52607559
[97] -0.96374520 0.78727015 -0.16110700 -1.35576439
> 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] -1.48448203 0.07990351 -1.22486474 0.49858768 0.62046660 0.43250490
[7] -0.99758437 0.75626948 0.32817090 -0.38059475 -1.16364295 -1.04980907
[13] 0.18961877 0.09129711 -0.41112573 0.07150415 0.28665540 1.35457321
[19] -0.64136440 -0.65126405 -0.49474314 1.76549197 2.04426852 -1.42354579
[25] 0.49204368 -1.28497965 1.54480805 1.29003638 -0.19163392 1.42787104
[31] 1.07023291 -0.91132308 -0.72773537 -1.85643042 0.02770917 -0.02253521
[37] -0.16904133 -1.34240903 -0.37637487 0.90329485 1.18283909 1.53360363
[43] 0.50609803 1.54146391 1.02757716 1.15943044 -2.46670372 0.57867402
[49] -0.19692680 -0.59351776 -0.44118895 -0.72432371 -1.96264170 -0.18690945
[55] 0.03642977 -1.93344204 1.34813094 1.79606423 -1.29512118 0.04493397
[61] 2.41114727 -1.39028680 -0.49672568 1.64362819 -0.82195892 -0.33640821
[67] 0.53321650 0.59767851 -0.87160498 -1.40432558 0.65082746 -0.06482052
[73] -1.03557179 -1.62790325 -0.01638941 0.99199181 1.29900256 0.67624165
[79] -0.02311490 1.03597807 -1.58690180 -0.37530741 0.20181335 0.43527974
[85] -1.19443859 -0.60130831 0.32649053 -0.69237298 -1.23884451 -0.79762439
[91] -0.28562769 0.21504201 -0.43385152 0.94868641 -1.42279879 -0.52607559
[97] -0.96374520 0.78727015 -0.16110700 -1.35576439
> rowMin(tmp2)
[1] -1.48448203 0.07990351 -1.22486474 0.49858768 0.62046660 0.43250490
[7] -0.99758437 0.75626948 0.32817090 -0.38059475 -1.16364295 -1.04980907
[13] 0.18961877 0.09129711 -0.41112573 0.07150415 0.28665540 1.35457321
[19] -0.64136440 -0.65126405 -0.49474314 1.76549197 2.04426852 -1.42354579
[25] 0.49204368 -1.28497965 1.54480805 1.29003638 -0.19163392 1.42787104
[31] 1.07023291 -0.91132308 -0.72773537 -1.85643042 0.02770917 -0.02253521
[37] -0.16904133 -1.34240903 -0.37637487 0.90329485 1.18283909 1.53360363
[43] 0.50609803 1.54146391 1.02757716 1.15943044 -2.46670372 0.57867402
[49] -0.19692680 -0.59351776 -0.44118895 -0.72432371 -1.96264170 -0.18690945
[55] 0.03642977 -1.93344204 1.34813094 1.79606423 -1.29512118 0.04493397
[61] 2.41114727 -1.39028680 -0.49672568 1.64362819 -0.82195892 -0.33640821
[67] 0.53321650 0.59767851 -0.87160498 -1.40432558 0.65082746 -0.06482052
[73] -1.03557179 -1.62790325 -0.01638941 0.99199181 1.29900256 0.67624165
[79] -0.02311490 1.03597807 -1.58690180 -0.37530741 0.20181335 0.43527974
[85] -1.19443859 -0.60130831 0.32649053 -0.69237298 -1.23884451 -0.79762439
[91] -0.28562769 0.21504201 -0.43385152 0.94868641 -1.42279879 -0.52607559
[97] -0.96374520 0.78727015 -0.16110700 -1.35576439
>
> colMeans(tmp2)
[1] -0.0754629
> colSums(tmp2)
[1] -7.54629
> colVars(tmp2)
[1] 1.068415
> colSd(tmp2)
[1] 1.033642
> colMax(tmp2)
[1] 2.411147
> colMin(tmp2)
[1] -2.466704
> colMedians(tmp2)
[1] -0.1129638
> colRanges(tmp2)
[,1]
[1,] -2.466704
[2,] 2.411147
>
> 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] 2.9131379 2.0735096 -0.2625320 -2.1689344 2.4665853 1.4224436
[7] 0.7228202 1.2365399 1.1179545 4.6910834
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.9464925
[2,] -0.3953292
[3,] 0.6014131
[4,] 1.0166475
[5,] 2.0993023
>
> rowApply(tmp,sum)
[1] 6.2771993 -1.6556653 3.4022829 -2.5916683 -2.0782842 -0.7013251
[7] 4.9896109 2.2830196 2.1513550 2.1360834
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 9 1 10 4 7 7 6 2 7
[2,] 4 10 3 4 10 4 6 4 8 2
[3,] 2 2 2 6 9 5 4 9 10 1
[4,] 1 5 4 8 2 8 1 10 6 3
[5,] 5 8 10 2 8 2 3 1 9 10
[6,] 3 4 5 9 6 9 2 3 7 4
[7,] 8 6 6 3 7 6 9 2 5 5
[8,] 7 1 8 1 3 10 5 8 3 9
[9,] 6 3 7 7 5 1 10 5 1 8
[10,] 10 7 9 5 1 3 8 7 4 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.0828881 2.3670132 -1.1576157 -0.9702988 2.7332708 1.9472059
[7] -1.1307223 -0.3448909 -3.5476209 0.4981083 -0.2496375 -0.2715364
[13] 2.7505653 1.5057798 -3.7133362 3.5074589 -2.8202058 0.8611139
[19] -4.4483479 -0.7427098
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.6916598
[2,] -0.9083621
[3,] -0.3025544
[4,] 0.2948363
[5,] 0.5248519
>
> rowApply(tmp,sum)
[1] 4.015892 -5.884412 1.023942 -1.375916 -3.088800
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 10 10 15 2 1
[2,] 20 8 16 4 18
[3,] 7 13 1 18 10
[4,] 12 2 12 13 16
[5,] 16 11 20 3 19
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.2948363 2.3559873 -0.20190819 0.449474879 1.1876569 0.06012722
[2,] -0.3025544 -0.7181533 -0.03509407 -1.968346644 -0.1761479 -1.01626033
[3,] 0.5248519 0.6708831 -1.76872015 0.028697689 1.7875262 -0.01543013
[4,] -0.9083621 -0.7437713 0.98928492 0.005612917 -0.8901339 1.30080355
[5,] -1.6916598 0.8020674 -0.14117826 0.514262355 0.8243694 1.61796562
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.33853069 1.12915920 0.2130416 -0.7564561 0.5254124 -2.9913212
[2,] -0.05544957 -0.01497348 -0.3549755 2.2803350 -1.4896403 1.4323068
[3,] -1.11067229 -0.53765130 -0.6495774 -0.2036002 1.6251391 0.5129389
[4,] -0.12605478 -0.64711408 -1.1783034 -0.2088209 -0.1868007 2.0513003
[5,] -0.17707635 -0.27431125 -1.5778062 -0.6133494 -0.7237481 -1.2767612
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 1.3778579 1.2888095 -0.4755185 1.6099484 -0.40670585 0.47946473
[2,] -0.8578170 0.6811542 -0.8934470 0.3475170 -2.18722011 0.09601433
[3,] 1.1173979 -0.2235937 -0.7301872 1.7450638 -0.75168195 -0.12277465
[4,] 0.7838253 -0.7133130 -0.6751640 -0.4029122 0.09580959 0.22072948
[5,] 0.3293013 0.4727228 -0.9390194 0.2078418 0.42959251 0.18768004
[,19] [,20]
[1,] -0.9044246 -1.5580808
[2,] -1.4928025 0.8411425
[3,] 0.1511575 -1.0258248
[4,] -0.5254760 0.3829444
[5,] -1.6768022 0.6171090
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 654 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -0.4467444 -0.1437796 -1.073656 -0.3141058 0.1400491 -1.957522 -1.314811
col8 col9 col10 col11 col12 col13
row1 -0.6444543 -0.5155733 -0.01456022 -1.441636 -0.4208942 -0.3706918
col14 col15 col16 col17 col18 col19 col20
row1 -0.9695895 -0.2892358 0.2719186 2.814608 -0.3356069 0.5466233 -1.074117
> tmp[,"col10"]
col10
row1 -0.01456022
row2 0.06863396
row3 1.53631272
row4 0.41464311
row5 -0.67777589
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -0.4467444 -0.1437796 -1.0736564 -0.3141058 0.1400491 -1.957521692
row5 -0.3169627 0.6726612 0.4872839 -0.2274106 -1.0869612 0.004417772
col7 col8 col9 col10 col11 col12
row1 -1.3148106 -0.6444543 -0.5155733 -0.01456022 -1.441636 -0.42089417
row5 -0.4143085 -0.6035996 -1.2455867 -0.67777589 1.587440 -0.04238367
col13 col14 col15 col16 col17 col18 col19
row1 -0.3706918 -0.9695895 -0.2892358 0.2719186 2.814608 -0.3356069 0.5466233
row5 -0.6575694 0.3861483 0.2001258 1.3254273 -1.001521 0.7862953 -0.1908364
col20
row1 -1.0741170
row5 0.9730344
> tmp[,c("col6","col20")]
col6 col20
row1 -1.957521692 -1.07411705
row2 0.781191232 1.54342387
row3 1.829018865 2.00166310
row4 0.808778344 -0.09702896
row5 0.004417772 0.97303441
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.957521692 -1.0741170
row5 0.004417772 0.9730344
>
>
>
>
> 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 48.66063 50.45106 49.90679 49.38548 49.81541 103.4949 50.54729 49.3085
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.50979 49.71552 50.79874 49.73692 50.48535 50.74585 47.54203 48.94239
col17 col18 col19 col20
row1 50.98597 51.12839 49.90104 104.0584
> tmp[,"col10"]
col10
row1 49.71552
row2 29.61365
row3 30.66077
row4 29.23898
row5 49.92423
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 48.66063 50.45106 49.90679 49.38548 49.81541 103.4949 50.54729 49.30850
row5 50.26529 49.44346 50.56688 49.64025 49.14192 104.6656 50.46717 49.80348
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.50979 49.71552 50.79874 49.73692 50.48535 50.74585 47.54203 48.94239
row5 48.78593 49.92423 49.92672 50.44329 49.04703 49.48843 48.49173 49.91866
col17 col18 col19 col20
row1 50.98597 51.12839 49.90104 104.0584
row5 50.71049 51.40362 51.12595 105.4323
> tmp[,c("col6","col20")]
col6 col20
row1 103.49488 104.05835
row2 72.84328 75.04503
row3 76.47154 72.66384
row4 74.93466 74.05094
row5 104.66564 105.43228
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.4949 104.0584
row5 104.6656 105.4323
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.4949 104.0584
row5 104.6656 105.4323
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.8473518
[2,] -0.6043313
[3,] 0.6817945
[4,] -1.1545162
[5,] 1.6247606
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.08654244 1.2583762
[2,] -2.13535895 0.8302442
[3,] 0.41360559 -0.1735580
[4,] -0.17781574 -0.2874313
[5,] 1.29911361 0.2866664
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 1.2383090 -0.26275896
[2,] -0.9754018 0.41892831
[3,] 0.1706807 -3.18757556
[4,] 0.1289880 1.41373799
[5,] -0.6778711 0.02013494
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 1.238309
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 1.2383090
[2,] -0.9754018
>
>
>
> 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 0.2895012 -1.160088 0.1330735 0.8225364 0.3262666 0.5713154 -1.0533995
row1 -1.0740258 0.548273 2.0999416 -1.1797139 -0.5709950 1.1996176 0.2959271
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.6860366 2.0874622 -1.267870 -1.0695260 -0.1867173 0.03979125
row1 0.4604530 -0.5050237 -1.182623 -0.2833334 0.8762367 -0.01986729
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 0.004946649 -0.6887939 0.7402649 -1.649001 0.6002067 -0.6744177 1.228707
row1 1.259686808 1.3843288 0.4842659 -0.038172 -0.4047224 -1.2087036 1.450436
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.2639625 -1.84451 1.204573 0.3491578 -0.6306395 0.1523949 0.03597256
[,8] [,9] [,10]
row2 -0.8394834 1.535226 -0.2129617
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 1.577762 -1.133542 0.08610028 -0.1842672 0.2980328 0.04381496 0.08493343
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.2799189 0.6544814 0.1681582 -1.333344 0.2590964 0.07898774 0.1156201
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.9731622 -1.108025 -1.528937 0.03651814 -1.174169 0.3868828
>
>
> 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: 0x5f1d65a1ff80>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d2424a3cba"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d2a38bb6e"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d27d5d509d"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d22ca39f2e"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d2572fb88a"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d247b3c638"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d28741b13"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d242df94c9"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d27620112b"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d263c2e201"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d2161c9ba2"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d242934739"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d22ebf02e2"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d27031dfad"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM3198d25ea86bfd"
>
>
> ### 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: 0x5f1d646155a0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5f1d646155a0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5f1d646155a0>
> rowMedians(tmp)
[1] 0.399025057 0.215304773 -0.442656227 -0.286585374 -0.269194811
[6] -0.152672284 -0.215806665 0.923790750 0.002981605 0.022887713
[11] -0.384476553 -0.604170550 -0.186895505 0.003358959 0.190957284
[16] 0.109134808 0.649314885 0.314960389 0.169674193 -0.854533419
[21] 0.293347378 0.520707156 -0.155426586 -0.416209853 0.191240486
[26] -0.114697494 -0.507056131 -0.069387975 0.307912804 0.019291845
[31] -0.078809656 0.233064280 0.017590889 0.728789138 0.423056045
[36] -0.258691388 -0.131276661 0.153634040 0.035511135 -0.252819199
[41] -0.152230279 -0.325500119 0.345595161 0.175180832 0.319944809
[46] -0.209708858 0.139766284 0.127782264 -0.323950286 0.084140000
[51] 0.002368353 -0.134681683 0.129293161 -0.131752335 0.236574955
[56] -0.123716872 0.196925089 -0.061925115 -0.252279633 0.271326147
[61] 0.412762422 -0.606258348 0.203142733 -0.266312641 -0.244984237
[66] 0.369032516 0.165354397 -0.405912657 -0.632328370 -0.021481092
[71] -0.043147379 0.548924592 -0.283577423 0.374266153 -0.333976230
[76] 0.219592173 -0.119312078 0.040443804 -0.224789244 0.214892904
[81] -0.021208730 0.349571777 -0.259001367 -0.495594239 -0.439769327
[86] 0.065000587 0.034150410 0.137281314 -0.174752644 -0.236345767
[91] 0.155580372 -0.059653044 -0.003246849 -0.031515868 0.780053445
[96] -0.684797685 -0.170838242 0.020863777 -0.548154704 0.221113866
[101] -0.128216246 -0.539379308 -0.236396143 -0.077988271 0.352639951
[106] -0.178403627 0.184948092 -0.754156416 0.264863780 -0.253298705
[111] 0.261078898 -0.327494970 -0.002508118 -0.149550910 -0.352977301
[116] -0.246685233 0.444164135 -0.011014567 0.213131592 -0.439501581
[121] -0.018834825 -0.405852844 -0.277549400 0.136780507 -0.034797429
[126] 0.075115271 0.268723318 -0.220542824 -0.335356878 -0.184840115
[131] 0.416274310 -0.191964708 -0.476718847 -0.542019231 -0.219669092
[136] 0.006523882 -0.339137468 -0.499301376 0.275863723 0.465570210
[141] -0.127431541 0.483685476 -0.179386101 0.587184187 0.010567893
[146] -0.115190691 0.228435100 -0.379665638 -0.427550515 -0.283743775
[151] 0.489517481 0.551088446 0.231639955 0.117741049 0.605344984
[156] -0.185855894 -0.203400881 0.158476050 0.212768438 0.007979471
[161] -0.317824417 -0.197692718 0.201174331 0.096530246 -0.289076146
[166] -0.204209623 0.197104655 -0.496329925 -0.110503590 0.291135456
[171] 0.195418956 -0.011957922 -0.042060308 0.045790421 -0.494922479
[176] -0.272474840 0.088229947 -0.271183724 -0.578530039 -0.258754647
[181] -0.069036892 -0.281393172 0.283913058 0.310702596 0.113284165
[186] -0.354795796 0.178360643 -0.495502572 -0.093825890 -0.041594322
[191] 0.050852061 -0.038502771 -0.190389063 0.721574234 -0.452853061
[196] -0.075611460 0.295884510 0.100672242 -0.131549161 0.206272296
[201] -0.222829917 0.048215515 -0.201047290 -0.422843355 0.225113127
[206] -0.053258093 0.515398870 -0.358333423 0.127961724 0.258418748
[211] 0.315029515 0.595136511 0.475488619 -0.350852293 -0.081890609
[216] 0.308063844 0.046868341 0.696719934 -0.132365059 -0.010034368
[221] 0.146106568 -0.312374960 0.309944553 0.061567493 0.099518739
[226] 0.016279098 -0.325086638 0.437851514 0.295249431 -0.691235558
>
> proc.time()
user system elapsed
1.395 1.469 2.854
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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: 0x5e618fc9e5f0>
> .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: 0x5e618fc9e5f0>
> .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: 0x5e618fc9e5f0>
> .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: 0x5e618fc9e5f0>
> 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: 0x5e619051c2b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e619051c2b0>
> .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: 0x5e619051c2b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e619051c2b0>
> .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: 0x5e619051c2b0>
> 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: 0x5e618fbffa20>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e618fbffa20>
> .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: 0x5e618fbffa20>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5e618fbffa20>
> .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: 0x5e618fbffa20>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5e618fbffa20>
> .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: 0x5e618fbffa20>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5e618fbffa20>
> .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: 0x5e618fbffa20>
> 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: 0x5e61903dce00>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5e61903dce00>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e61903dce00>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e61903dce00>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile319aba2b91248d" "BufferedMatrixFile319aba54a37838"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile319aba2b91248d" "BufferedMatrixFile319aba54a37838"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e61902e44c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e61902e44c0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5e61902e44c0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5e61902e44c0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5e61902e44c0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5e61902e44c0>
> .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: 0x5e619068d7e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e619068d7e0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5e619068d7e0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5e619068d7e0>
> 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: 0x5e6191766520>
> .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: 0x5e6191766520>
> rm(P)
>
> proc.time()
user system elapsed
0.271 0.056 0.316
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
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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
0.241 0.050 0.280