Ben Bolstad
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| 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 2024-11-20 12:05 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.70.0.tar.gz |
| StartedAt: 2024-11-19 20:09:47 -0500 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 20:14:05 -0500 (Tue, 19 Nov 2024) |
| EllapsedTime: 258.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.70.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.70.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... WARNING
Found the following significant warnings:
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.237 0.101 0.341
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/Users/biocbuild/bbs-3.20-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) limit (Mb) max used (Mb)
Ncells 474173 25.4 1035465 55.3 NA 638628 34.2
Vcells 877659 6.7 8388608 64.0 98304 2071890 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] "Tue Nov 19 20:13:47 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Nov 19 20:13:47 2024"
>
>
> 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: 0x600000f4c420>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Nov 19 20:13:50 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Nov 19 20:13:51 2024"
>
> ColMode(tmp2)
<pointer: 0x600000f4c420>
>
>
>
> ### 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,] 99.7792039 1.14168526 -1.1194570 0.21983188
[2,] -1.2285104 -0.05091759 -0.5862434 0.04190634
[3,] 0.5419467 1.04362522 -0.3483615 1.02912893
[4,] 1.4984558 -1.07473960 0.3005486 -1.75732611
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-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,] 99.7792039 1.14168526 1.1194570 0.21983188
[2,] 1.2285104 0.05091759 0.5862434 0.04190634
[3,] 0.5419467 1.04362522 0.3483615 1.02912893
[4,] 1.4984558 1.07473960 0.3005486 1.75732611
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-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,] 9.9889541 1.0684967 1.0580440 0.4688623
[2,] 1.1083819 0.2256493 0.7656653 0.2047104
[3,] 0.7361703 1.0215798 0.5902216 1.0144599
[4,] 1.2241143 1.0366965 0.5482231 1.3256418
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.66874 36.82665 36.69990 29.90846
[2,] 37.31233 27.30741 33.24290 27.08901
[3,] 32.90365 36.25942 31.25058 36.17373
[4,] 38.73960 36.44170 30.78278 40.01374
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600000f6c000>
> exp(tmp5)
<pointer: 0x600000f6c000>
> log(tmp5,2)
<pointer: 0x600000f6c000>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 467.6186
> Min(tmp5)
[1] 52.96526
> mean(tmp5)
[1] 71.98576
> Sum(tmp5)
[1] 14397.15
> Var(tmp5)
[1] 860.4526
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.79145 67.70244 70.30842 71.48570 68.88631 67.92958 72.51219 67.44339
[9] 71.68223 72.11585
> rowSums(tmp5)
[1] 1795.829 1354.049 1406.168 1429.714 1377.726 1358.592 1450.244 1348.868
[9] 1433.645 1442.317
> rowVars(tmp5)
[1] 7980.92757 60.91307 60.37905 44.30870 68.14702 66.27727
[7] 69.93138 62.86210 63.38972 129.15045
> rowSd(tmp5)
[1] 89.336037 7.804683 7.770395 6.656478 8.255121 8.141085 8.362498
[8] 7.928562 7.961766 11.364438
> rowMax(tmp5)
[1] 467.61856 80.92813 87.85674 83.28337 88.96339 83.84130 87.05033
[8] 88.17558 91.36558 95.57841
> rowMin(tmp5)
[1] 57.23686 54.74594 54.75381 59.70472 57.13144 54.91362 55.43561 57.78701
[9] 60.63583 52.96526
>
> colMeans(tmp5)
[1] 112.33364 69.39478 69.96158 65.83738 71.21228 68.18470 67.73204
[8] 68.59335 70.03036 73.27054 68.52082 72.27003 67.62886 77.10689
[15] 71.42870 69.19311 76.44552 68.16270 66.02298 66.38487
> colSums(tmp5)
[1] 1123.3364 693.9478 699.6158 658.3738 712.1228 681.8470 677.3204
[8] 685.9335 700.3036 732.7054 685.2082 722.7003 676.2886 771.0689
[15] 714.2870 691.9311 764.4552 681.6270 660.2298 663.8487
> colVars(tmp5)
[1] 15622.05354 114.60490 76.14879 76.09507 151.68930 45.44752
[7] 60.28050 42.36138 28.65050 81.27975 62.76207 101.75606
[13] 49.21766 58.93917 40.60616 38.66439 89.36645 79.38832
[19] 34.06232 68.27626
> colSd(tmp5)
[1] 124.988214 10.705368 8.726327 8.723249 12.316221 6.741478
[7] 7.764052 6.508562 5.352616 9.015528 7.922252 10.087421
[13] 7.015530 7.677185 6.372297 6.218069 9.453383 8.910013
[19] 5.836293 8.262945
> colMax(tmp5)
[1] 467.61856 83.54438 91.36558 83.28337 95.57841 78.61868 79.81938
[8] 77.54776 79.56837 88.96339 76.54035 87.89420 77.03149 87.85674
[15] 83.73080 82.95519 88.17558 82.14758 78.55118 81.49500
> colMin(tmp5)
[1] 63.86284 56.83680 63.04130 56.38223 55.43561 57.99357 56.07401 54.74594
[9] 64.04664 59.83168 54.91362 58.24938 57.78701 64.13741 62.96363 60.00028
[17] 57.13144 52.96526 58.45718 54.75381
>
>
> ### 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] 89.79145 67.70244 70.30842 71.48570 68.88631 67.92958 NA 67.44339
[9] 71.68223 72.11585
> rowSums(tmp5)
[1] 1795.829 1354.049 1406.168 1429.714 1377.726 1358.592 NA 1348.868
[9] 1433.645 1442.317
> rowVars(tmp5)
[1] 7980.92757 60.91307 60.37905 44.30870 68.14702 66.27727
[7] 66.45639 62.86210 63.38972 129.15045
> rowSd(tmp5)
[1] 89.336037 7.804683 7.770395 6.656478 8.255121 8.141085 8.152079
[8] 7.928562 7.961766 11.364438
> rowMax(tmp5)
[1] 467.61856 80.92813 87.85674 83.28337 88.96339 83.84130 NA
[8] 88.17558 91.36558 95.57841
> rowMin(tmp5)
[1] 57.23686 54.74594 54.75381 59.70472 57.13144 54.91362 NA 57.78701
[9] 60.63583 52.96526
>
> colMeans(tmp5)
[1] 112.33364 69.39478 69.96158 65.83738 71.21228 68.18470 67.73204
[8] 68.59335 70.03036 73.27054 68.52082 72.27003 67.62886 77.10689
[15] NA 69.19311 76.44552 68.16270 66.02298 66.38487
> colSums(tmp5)
[1] 1123.3364 693.9478 699.6158 658.3738 712.1228 681.8470 677.3204
[8] 685.9335 700.3036 732.7054 685.2082 722.7003 676.2886 771.0689
[15] NA 691.9311 764.4552 681.6270 660.2298 663.8487
> colVars(tmp5)
[1] 15622.05354 114.60490 76.14879 76.09507 151.68930 45.44752
[7] 60.28050 42.36138 28.65050 81.27975 62.76207 101.75606
[13] 49.21766 58.93917 NA 38.66439 89.36645 79.38832
[19] 34.06232 68.27626
> colSd(tmp5)
[1] 124.988214 10.705368 8.726327 8.723249 12.316221 6.741478
[7] 7.764052 6.508562 5.352616 9.015528 7.922252 10.087421
[13] 7.015530 7.677185 NA 6.218069 9.453383 8.910013
[19] 5.836293 8.262945
> colMax(tmp5)
[1] 467.61856 83.54438 91.36558 83.28337 95.57841 78.61868 79.81938
[8] 77.54776 79.56837 88.96339 76.54035 87.89420 77.03149 87.85674
[15] NA 82.95519 88.17558 82.14758 78.55118 81.49500
> colMin(tmp5)
[1] 63.86284 56.83680 63.04130 56.38223 55.43561 57.99357 56.07401 54.74594
[9] 64.04664 59.83168 54.91362 58.24938 57.78701 64.13741 NA 60.00028
[17] 57.13144 52.96526 58.45718 54.75381
>
> Max(tmp5,na.rm=TRUE)
[1] 467.6186
> Min(tmp5,na.rm=TRUE)
[1] 52.96526
> mean(tmp5,na.rm=TRUE)
[1] 71.92674
> Sum(tmp5,na.rm=TRUE)
[1] 14313.42
> Var(tmp5,na.rm=TRUE)
[1] 864.0981
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.79145 67.70244 70.30842 71.48570 68.88631 67.92958 71.92174 67.44339
[9] 71.68223 72.11585
> rowSums(tmp5,na.rm=TRUE)
[1] 1795.829 1354.049 1406.168 1429.714 1377.726 1358.592 1366.513 1348.868
[9] 1433.645 1442.317
> rowVars(tmp5,na.rm=TRUE)
[1] 7980.92757 60.91307 60.37905 44.30870 68.14702 66.27727
[7] 66.45639 62.86210 63.38972 129.15045
> rowSd(tmp5,na.rm=TRUE)
[1] 89.336037 7.804683 7.770395 6.656478 8.255121 8.141085 8.152079
[8] 7.928562 7.961766 11.364438
> rowMax(tmp5,na.rm=TRUE)
[1] 467.61856 80.92813 87.85674 83.28337 88.96339 83.84130 87.05033
[8] 88.17558 91.36558 95.57841
> rowMin(tmp5,na.rm=TRUE)
[1] 57.23686 54.74594 54.75381 59.70472 57.13144 54.91362 55.43561 57.78701
[9] 60.63583 52.96526
>
> colMeans(tmp5,na.rm=TRUE)
[1] 112.33364 69.39478 69.96158 65.83738 71.21228 68.18470 67.73204
[8] 68.59335 70.03036 73.27054 68.52082 72.27003 67.62886 77.10689
[15] 70.06180 69.19311 76.44552 68.16270 66.02298 66.38487
> colSums(tmp5,na.rm=TRUE)
[1] 1123.3364 693.9478 699.6158 658.3738 712.1228 681.8470 677.3204
[8] 685.9335 700.3036 732.7054 685.2082 722.7003 676.2886 771.0689
[15] 630.5562 691.9311 764.4552 681.6270 660.2298 663.8487
> colVars(tmp5,na.rm=TRUE)
[1] 15622.05354 114.60490 76.14879 76.09507 151.68930 45.44752
[7] 60.28050 42.36138 28.65050 81.27975 62.76207 101.75606
[13] 49.21766 58.93917 24.66226 38.66439 89.36645 79.38832
[19] 34.06232 68.27626
> colSd(tmp5,na.rm=TRUE)
[1] 124.988214 10.705368 8.726327 8.723249 12.316221 6.741478
[7] 7.764052 6.508562 5.352616 9.015528 7.922252 10.087421
[13] 7.015530 7.677185 4.966111 6.218069 9.453383 8.910013
[19] 5.836293 8.262945
> colMax(tmp5,na.rm=TRUE)
[1] 467.61856 83.54438 91.36558 83.28337 95.57841 78.61868 79.81938
[8] 77.54776 79.56837 88.96339 76.54035 87.89420 77.03149 87.85674
[15] 77.92809 82.95519 88.17558 82.14758 78.55118 81.49500
> colMin(tmp5,na.rm=TRUE)
[1] 63.86284 56.83680 63.04130 56.38223 55.43561 57.99357 56.07401 54.74594
[9] 64.04664 59.83168 54.91362 58.24938 57.78701 64.13741 62.96363 60.00028
[17] 57.13144 52.96526 58.45718 54.75381
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.79145 67.70244 70.30842 71.48570 68.88631 67.92958 NaN 67.44339
[9] 71.68223 72.11585
> rowSums(tmp5,na.rm=TRUE)
[1] 1795.829 1354.049 1406.168 1429.714 1377.726 1358.592 0.000 1348.868
[9] 1433.645 1442.317
> rowVars(tmp5,na.rm=TRUE)
[1] 7980.92757 60.91307 60.37905 44.30870 68.14702 66.27727
[7] NA 62.86210 63.38972 129.15045
> rowSd(tmp5,na.rm=TRUE)
[1] 89.336037 7.804683 7.770395 6.656478 8.255121 8.141085 NA
[8] 7.928562 7.961766 11.364438
> rowMax(tmp5,na.rm=TRUE)
[1] 467.61856 80.92813 87.85674 83.28337 88.96339 83.84130 NA
[8] 88.17558 91.36558 95.57841
> rowMin(tmp5,na.rm=TRUE)
[1] 57.23686 54.74594 54.75381 59.70472 57.13144 54.91362 NA 57.78701
[9] 60.63583 52.96526
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.52166 67.89437 70.51536 66.35513 72.96525 68.13194 66.97778
[8] 68.71430 68.97058 74.22100 67.81954 70.62778 67.11339 76.35015
[15] NaN 68.65776 76.36088 67.82260 66.05966 66.40437
> colSums(tmp5,na.rm=TRUE)
[1] 1048.6949 611.0493 634.6382 597.1962 656.6872 613.1874 602.8000
[8] 618.4287 620.7352 667.9890 610.3758 635.6500 604.0205 687.1514
[15] 0.0000 617.9198 687.2479 610.4034 594.5370 597.6394
> colVars(tmp5,na.rm=TRUE)
[1] 17377.49121 103.60398 82.21736 82.59119 136.08053 51.09714
[7] 61.41525 47.49197 19.59658 81.27683 65.07459 84.13429
[13] 52.38067 59.86429 NA 40.27317 100.45665 88.01053
[19] 38.30497 76.80651
> colSd(tmp5,na.rm=TRUE)
[1] 131.823713 10.178604 9.067379 9.087969 11.665356 7.148227
[7] 7.836788 6.891442 4.426802 9.015366 8.066882 9.172475
[13] 7.237449 7.737201 NA 6.346115 10.022807 9.381393
[19] 6.189101 8.763932
> colMax(tmp5,na.rm=TRUE)
[1] 467.61856 83.54438 91.36558 83.28337 95.57841 78.61868 79.81938
[8] 77.54776 77.54778 88.96339 76.54035 87.89420 77.03149 87.85674
[15] -Inf 82.95519 88.17558 82.14758 78.55118 81.49500
> colMin(tmp5,na.rm=TRUE)
[1] 63.86284 56.83680 63.04130 56.38223 59.70472 57.99357 56.07401 54.74594
[9] 64.04664 59.83168 54.91362 58.24938 57.78701 64.13741 Inf 60.00028
[17] 57.13144 52.96526 58.45718 54.75381
>
>
>
>
> 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] 254.6159 235.6298 281.4234 228.4352 175.5727 152.3328 209.5780 221.5983
[9] 200.0753 186.3796
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 254.6159 235.6298 281.4234 228.4352 175.5727 152.3328 209.5780 221.5983
[9] 200.0753 186.3796
>
>
>
> 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] 0.000000e+00 -5.684342e-14 -5.684342e-14 -8.526513e-14 9.947598e-14
[6] -1.136868e-13 5.684342e-14 5.684342e-14 -4.263256e-14 1.136868e-13
[11] 2.131628e-14 -2.842171e-14 2.842171e-14 1.136868e-13 8.526513e-14
[16] -8.526513e-14 5.684342e-14 0.000000e+00 -8.526513e-14 -1.136868e-13
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
10 12
2 11
2 9
7 12
7 2
10 1
5 11
9 10
7 5
2 8
6 14
2 1
10 11
4 7
9 3
10 13
1 11
5 17
8 9
1 16
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] 3.302781
> Min(tmp)
[1] -2.909
> mean(tmp)
[1] 0.253572
> Sum(tmp)
[1] 25.3572
> Var(tmp)
[1] 1.182602
>
> rowMeans(tmp)
[1] 0.253572
> rowSums(tmp)
[1] 25.3572
> rowVars(tmp)
[1] 1.182602
> rowSd(tmp)
[1] 1.087475
> rowMax(tmp)
[1] 3.302781
> rowMin(tmp)
[1] -2.909
>
> colMeans(tmp)
[1] 0.80078139 0.33393578 0.11043458 0.86362250 -0.40663538 -0.87098949
[7] -1.01186927 -1.44560993 1.30554843 2.24792551 -0.28387364 -0.83407229
[13] -0.89096500 -0.20706307 0.80580736 0.99263488 -0.63228897 -0.43741483
[19] -1.04860357 -1.14927946 0.14020239 0.82463059 -0.20798292 -2.00514018
[25] 0.45063404 -1.38673655 -0.12263955 0.47753576 1.91240094 0.65435667
[31] -2.90899965 0.14031162 -0.93052853 0.30800434 2.08494765 -0.73494138
[37] 1.86445802 0.57327706 1.13952557 0.43399190 0.83037752 -0.73891288
[43] -0.47605573 0.52702287 -0.49200510 -0.64121126 0.77995234 1.62312866
[49] 0.37478609 0.74535628 1.80877887 2.79054412 -0.46342054 0.02141008
[55] 0.81342879 0.32817102 -0.39937259 -0.25714992 0.31637169 1.42878274
[61] 2.46467234 -1.11239283 1.70308015 0.11131688 1.50998102 0.12654708
[67] 0.03680273 -0.94208452 2.29967524 1.06555569 -0.13171822 -0.41801422
[73] 3.30278119 1.22356589 -0.96224632 0.91555723 -0.13813381 -1.19414922
[79] -1.31609693 -0.04685506 0.40956736 0.97177458 0.79550627 0.79526830
[85] 0.90645218 -0.04287469 2.31004901 0.14304921 -0.70029550 -0.70591703
[91] -1.04790962 -0.53280898 1.32659372 0.15079108 -0.69426929 1.09345292
[97] 0.54687633 1.02516039 0.44975253 -0.21018003
> colSums(tmp)
[1] 0.80078139 0.33393578 0.11043458 0.86362250 -0.40663538 -0.87098949
[7] -1.01186927 -1.44560993 1.30554843 2.24792551 -0.28387364 -0.83407229
[13] -0.89096500 -0.20706307 0.80580736 0.99263488 -0.63228897 -0.43741483
[19] -1.04860357 -1.14927946 0.14020239 0.82463059 -0.20798292 -2.00514018
[25] 0.45063404 -1.38673655 -0.12263955 0.47753576 1.91240094 0.65435667
[31] -2.90899965 0.14031162 -0.93052853 0.30800434 2.08494765 -0.73494138
[37] 1.86445802 0.57327706 1.13952557 0.43399190 0.83037752 -0.73891288
[43] -0.47605573 0.52702287 -0.49200510 -0.64121126 0.77995234 1.62312866
[49] 0.37478609 0.74535628 1.80877887 2.79054412 -0.46342054 0.02141008
[55] 0.81342879 0.32817102 -0.39937259 -0.25714992 0.31637169 1.42878274
[61] 2.46467234 -1.11239283 1.70308015 0.11131688 1.50998102 0.12654708
[67] 0.03680273 -0.94208452 2.29967524 1.06555569 -0.13171822 -0.41801422
[73] 3.30278119 1.22356589 -0.96224632 0.91555723 -0.13813381 -1.19414922
[79] -1.31609693 -0.04685506 0.40956736 0.97177458 0.79550627 0.79526830
[85] 0.90645218 -0.04287469 2.31004901 0.14304921 -0.70029550 -0.70591703
[91] -1.04790962 -0.53280898 1.32659372 0.15079108 -0.69426929 1.09345292
[97] 0.54687633 1.02516039 0.44975253 -0.21018003
> 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] 0.80078139 0.33393578 0.11043458 0.86362250 -0.40663538 -0.87098949
[7] -1.01186927 -1.44560993 1.30554843 2.24792551 -0.28387364 -0.83407229
[13] -0.89096500 -0.20706307 0.80580736 0.99263488 -0.63228897 -0.43741483
[19] -1.04860357 -1.14927946 0.14020239 0.82463059 -0.20798292 -2.00514018
[25] 0.45063404 -1.38673655 -0.12263955 0.47753576 1.91240094 0.65435667
[31] -2.90899965 0.14031162 -0.93052853 0.30800434 2.08494765 -0.73494138
[37] 1.86445802 0.57327706 1.13952557 0.43399190 0.83037752 -0.73891288
[43] -0.47605573 0.52702287 -0.49200510 -0.64121126 0.77995234 1.62312866
[49] 0.37478609 0.74535628 1.80877887 2.79054412 -0.46342054 0.02141008
[55] 0.81342879 0.32817102 -0.39937259 -0.25714992 0.31637169 1.42878274
[61] 2.46467234 -1.11239283 1.70308015 0.11131688 1.50998102 0.12654708
[67] 0.03680273 -0.94208452 2.29967524 1.06555569 -0.13171822 -0.41801422
[73] 3.30278119 1.22356589 -0.96224632 0.91555723 -0.13813381 -1.19414922
[79] -1.31609693 -0.04685506 0.40956736 0.97177458 0.79550627 0.79526830
[85] 0.90645218 -0.04287469 2.31004901 0.14304921 -0.70029550 -0.70591703
[91] -1.04790962 -0.53280898 1.32659372 0.15079108 -0.69426929 1.09345292
[97] 0.54687633 1.02516039 0.44975253 -0.21018003
> colMin(tmp)
[1] 0.80078139 0.33393578 0.11043458 0.86362250 -0.40663538 -0.87098949
[7] -1.01186927 -1.44560993 1.30554843 2.24792551 -0.28387364 -0.83407229
[13] -0.89096500 -0.20706307 0.80580736 0.99263488 -0.63228897 -0.43741483
[19] -1.04860357 -1.14927946 0.14020239 0.82463059 -0.20798292 -2.00514018
[25] 0.45063404 -1.38673655 -0.12263955 0.47753576 1.91240094 0.65435667
[31] -2.90899965 0.14031162 -0.93052853 0.30800434 2.08494765 -0.73494138
[37] 1.86445802 0.57327706 1.13952557 0.43399190 0.83037752 -0.73891288
[43] -0.47605573 0.52702287 -0.49200510 -0.64121126 0.77995234 1.62312866
[49] 0.37478609 0.74535628 1.80877887 2.79054412 -0.46342054 0.02141008
[55] 0.81342879 0.32817102 -0.39937259 -0.25714992 0.31637169 1.42878274
[61] 2.46467234 -1.11239283 1.70308015 0.11131688 1.50998102 0.12654708
[67] 0.03680273 -0.94208452 2.29967524 1.06555569 -0.13171822 -0.41801422
[73] 3.30278119 1.22356589 -0.96224632 0.91555723 -0.13813381 -1.19414922
[79] -1.31609693 -0.04685506 0.40956736 0.97177458 0.79550627 0.79526830
[85] 0.90645218 -0.04287469 2.31004901 0.14304921 -0.70029550 -0.70591703
[91] -1.04790962 -0.53280898 1.32659372 0.15079108 -0.69426929 1.09345292
[97] 0.54687633 1.02516039 0.44975253 -0.21018003
> colMedians(tmp)
[1] 0.80078139 0.33393578 0.11043458 0.86362250 -0.40663538 -0.87098949
[7] -1.01186927 -1.44560993 1.30554843 2.24792551 -0.28387364 -0.83407229
[13] -0.89096500 -0.20706307 0.80580736 0.99263488 -0.63228897 -0.43741483
[19] -1.04860357 -1.14927946 0.14020239 0.82463059 -0.20798292 -2.00514018
[25] 0.45063404 -1.38673655 -0.12263955 0.47753576 1.91240094 0.65435667
[31] -2.90899965 0.14031162 -0.93052853 0.30800434 2.08494765 -0.73494138
[37] 1.86445802 0.57327706 1.13952557 0.43399190 0.83037752 -0.73891288
[43] -0.47605573 0.52702287 -0.49200510 -0.64121126 0.77995234 1.62312866
[49] 0.37478609 0.74535628 1.80877887 2.79054412 -0.46342054 0.02141008
[55] 0.81342879 0.32817102 -0.39937259 -0.25714992 0.31637169 1.42878274
[61] 2.46467234 -1.11239283 1.70308015 0.11131688 1.50998102 0.12654708
[67] 0.03680273 -0.94208452 2.29967524 1.06555569 -0.13171822 -0.41801422
[73] 3.30278119 1.22356589 -0.96224632 0.91555723 -0.13813381 -1.19414922
[79] -1.31609693 -0.04685506 0.40956736 0.97177458 0.79550627 0.79526830
[85] 0.90645218 -0.04287469 2.31004901 0.14304921 -0.70029550 -0.70591703
[91] -1.04790962 -0.53280898 1.32659372 0.15079108 -0.69426929 1.09345292
[97] 0.54687633 1.02516039 0.44975253 -0.21018003
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.8007814 0.3339358 0.1104346 0.8636225 -0.4066354 -0.8709895 -1.011869
[2,] 0.8007814 0.3339358 0.1104346 0.8636225 -0.4066354 -0.8709895 -1.011869
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.44561 1.305548 2.247926 -0.2838736 -0.8340723 -0.890965 -0.2070631
[2,] -1.44561 1.305548 2.247926 -0.2838736 -0.8340723 -0.890965 -0.2070631
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.8058074 0.9926349 -0.632289 -0.4374148 -1.048604 -1.149279 0.1402024
[2,] 0.8058074 0.9926349 -0.632289 -0.4374148 -1.048604 -1.149279 0.1402024
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.8246306 -0.2079829 -2.00514 0.450634 -1.386737 -0.1226395 0.4775358
[2,] 0.8246306 -0.2079829 -2.00514 0.450634 -1.386737 -0.1226395 0.4775358
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.912401 0.6543567 -2.909 0.1403116 -0.9305285 0.3080043 2.084948
[2,] 1.912401 0.6543567 -2.909 0.1403116 -0.9305285 0.3080043 2.084948
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.7349414 1.864458 0.5732771 1.139526 0.4339919 0.8303775 -0.7389129
[2,] -0.7349414 1.864458 0.5732771 1.139526 0.4339919 0.8303775 -0.7389129
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.4760557 0.5270229 -0.4920051 -0.6412113 0.7799523 1.623129 0.3747861
[2,] -0.4760557 0.5270229 -0.4920051 -0.6412113 0.7799523 1.623129 0.3747861
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.7453563 1.808779 2.790544 -0.4634205 0.02141008 0.8134288 0.328171
[2,] 0.7453563 1.808779 2.790544 -0.4634205 0.02141008 0.8134288 0.328171
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.3993726 -0.2571499 0.3163717 1.428783 2.464672 -1.112393 1.70308
[2,] -0.3993726 -0.2571499 0.3163717 1.428783 2.464672 -1.112393 1.70308
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.1113169 1.509981 0.1265471 0.03680273 -0.9420845 2.299675 1.065556
[2,] 0.1113169 1.509981 0.1265471 0.03680273 -0.9420845 2.299675 1.065556
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.1317182 -0.4180142 3.302781 1.223566 -0.9622463 0.9155572 -0.1381338
[2,] -0.1317182 -0.4180142 3.302781 1.223566 -0.9622463 0.9155572 -0.1381338
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.194149 -1.316097 -0.04685506 0.4095674 0.9717746 0.7955063 0.7952683
[2,] -1.194149 -1.316097 -0.04685506 0.4095674 0.9717746 0.7955063 0.7952683
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.9064522 -0.04287469 2.310049 0.1430492 -0.7002955 -0.705917 -1.04791
[2,] 0.9064522 -0.04287469 2.310049 0.1430492 -0.7002955 -0.705917 -1.04791
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.532809 1.326594 0.1507911 -0.6942693 1.093453 0.5468763 1.02516
[2,] -0.532809 1.326594 0.1507911 -0.6942693 1.093453 0.5468763 1.02516
[,99] [,100]
[1,] 0.4497525 -0.21018
[2,] 0.4497525 -0.21018
>
>
> Max(tmp2)
[1] 2.579912
> Min(tmp2)
[1] -2.380263
> mean(tmp2)
[1] -0.08906359
> Sum(tmp2)
[1] -8.906359
> Var(tmp2)
[1] 1.137425
>
> rowMeans(tmp2)
[1] 0.92105816 1.73816864 0.74817209 -0.25862893 0.16230721 -0.99897568
[7] 0.02837893 0.89374281 -0.09678025 0.28566775 1.27448125 0.32117878
[13] -0.33525678 0.65092467 0.40259237 -0.31245978 -0.36367195 1.23804831
[19] -0.35679379 -1.31296514 0.02097813 -1.21484998 0.73251422 -1.29008439
[25] -0.77940225 -1.67058147 0.38379171 -1.92932062 -1.36138477 -0.51027055
[31] 2.57991210 0.72620548 0.60503412 2.04471446 0.41695760 -0.48209767
[37] 0.25655636 -0.50543819 -0.65990410 -0.07866296 -0.33832904 -1.62254186
[43] 0.33714178 -1.61633323 -0.19350228 0.60688450 -0.19859581 -1.30252270
[49] 1.18325465 2.00258560 -0.11445069 1.61975130 0.22816700 0.64711760
[55] -2.09772515 -1.64229132 -0.90950534 0.23367355 -2.38026292 -0.40340496
[61] 0.42497255 -0.72007522 -2.34534271 -0.42665444 -0.82003291 -2.10784612
[67] -0.22120357 -0.37120597 -0.37700934 1.65663742 -0.83435066 -0.27735939
[73] -1.00879113 -0.93772751 1.59863126 -0.22488918 0.71850238 1.56985469
[79] -0.06440576 -0.97368825 -0.68149808 -0.31692341 1.42497049 0.52862365
[85] -2.06590494 0.62369937 0.58441358 0.98524372 -0.33922242 -1.56467848
[91] 0.74526470 -0.67104911 0.51495653 -0.47039568 0.04610017 1.01975058
[97] 2.15132066 -1.35774116 -0.77673295 0.50246096
> rowSums(tmp2)
[1] 0.92105816 1.73816864 0.74817209 -0.25862893 0.16230721 -0.99897568
[7] 0.02837893 0.89374281 -0.09678025 0.28566775 1.27448125 0.32117878
[13] -0.33525678 0.65092467 0.40259237 -0.31245978 -0.36367195 1.23804831
[19] -0.35679379 -1.31296514 0.02097813 -1.21484998 0.73251422 -1.29008439
[25] -0.77940225 -1.67058147 0.38379171 -1.92932062 -1.36138477 -0.51027055
[31] 2.57991210 0.72620548 0.60503412 2.04471446 0.41695760 -0.48209767
[37] 0.25655636 -0.50543819 -0.65990410 -0.07866296 -0.33832904 -1.62254186
[43] 0.33714178 -1.61633323 -0.19350228 0.60688450 -0.19859581 -1.30252270
[49] 1.18325465 2.00258560 -0.11445069 1.61975130 0.22816700 0.64711760
[55] -2.09772515 -1.64229132 -0.90950534 0.23367355 -2.38026292 -0.40340496
[61] 0.42497255 -0.72007522 -2.34534271 -0.42665444 -0.82003291 -2.10784612
[67] -0.22120357 -0.37120597 -0.37700934 1.65663742 -0.83435066 -0.27735939
[73] -1.00879113 -0.93772751 1.59863126 -0.22488918 0.71850238 1.56985469
[79] -0.06440576 -0.97368825 -0.68149808 -0.31692341 1.42497049 0.52862365
[85] -2.06590494 0.62369937 0.58441358 0.98524372 -0.33922242 -1.56467848
[91] 0.74526470 -0.67104911 0.51495653 -0.47039568 0.04610017 1.01975058
[97] 2.15132066 -1.35774116 -0.77673295 0.50246096
> 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] 0.92105816 1.73816864 0.74817209 -0.25862893 0.16230721 -0.99897568
[7] 0.02837893 0.89374281 -0.09678025 0.28566775 1.27448125 0.32117878
[13] -0.33525678 0.65092467 0.40259237 -0.31245978 -0.36367195 1.23804831
[19] -0.35679379 -1.31296514 0.02097813 -1.21484998 0.73251422 -1.29008439
[25] -0.77940225 -1.67058147 0.38379171 -1.92932062 -1.36138477 -0.51027055
[31] 2.57991210 0.72620548 0.60503412 2.04471446 0.41695760 -0.48209767
[37] 0.25655636 -0.50543819 -0.65990410 -0.07866296 -0.33832904 -1.62254186
[43] 0.33714178 -1.61633323 -0.19350228 0.60688450 -0.19859581 -1.30252270
[49] 1.18325465 2.00258560 -0.11445069 1.61975130 0.22816700 0.64711760
[55] -2.09772515 -1.64229132 -0.90950534 0.23367355 -2.38026292 -0.40340496
[61] 0.42497255 -0.72007522 -2.34534271 -0.42665444 -0.82003291 -2.10784612
[67] -0.22120357 -0.37120597 -0.37700934 1.65663742 -0.83435066 -0.27735939
[73] -1.00879113 -0.93772751 1.59863126 -0.22488918 0.71850238 1.56985469
[79] -0.06440576 -0.97368825 -0.68149808 -0.31692341 1.42497049 0.52862365
[85] -2.06590494 0.62369937 0.58441358 0.98524372 -0.33922242 -1.56467848
[91] 0.74526470 -0.67104911 0.51495653 -0.47039568 0.04610017 1.01975058
[97] 2.15132066 -1.35774116 -0.77673295 0.50246096
> rowMin(tmp2)
[1] 0.92105816 1.73816864 0.74817209 -0.25862893 0.16230721 -0.99897568
[7] 0.02837893 0.89374281 -0.09678025 0.28566775 1.27448125 0.32117878
[13] -0.33525678 0.65092467 0.40259237 -0.31245978 -0.36367195 1.23804831
[19] -0.35679379 -1.31296514 0.02097813 -1.21484998 0.73251422 -1.29008439
[25] -0.77940225 -1.67058147 0.38379171 -1.92932062 -1.36138477 -0.51027055
[31] 2.57991210 0.72620548 0.60503412 2.04471446 0.41695760 -0.48209767
[37] 0.25655636 -0.50543819 -0.65990410 -0.07866296 -0.33832904 -1.62254186
[43] 0.33714178 -1.61633323 -0.19350228 0.60688450 -0.19859581 -1.30252270
[49] 1.18325465 2.00258560 -0.11445069 1.61975130 0.22816700 0.64711760
[55] -2.09772515 -1.64229132 -0.90950534 0.23367355 -2.38026292 -0.40340496
[61] 0.42497255 -0.72007522 -2.34534271 -0.42665444 -0.82003291 -2.10784612
[67] -0.22120357 -0.37120597 -0.37700934 1.65663742 -0.83435066 -0.27735939
[73] -1.00879113 -0.93772751 1.59863126 -0.22488918 0.71850238 1.56985469
[79] -0.06440576 -0.97368825 -0.68149808 -0.31692341 1.42497049 0.52862365
[85] -2.06590494 0.62369937 0.58441358 0.98524372 -0.33922242 -1.56467848
[91] 0.74526470 -0.67104911 0.51495653 -0.47039568 0.04610017 1.01975058
[97] 2.15132066 -1.35774116 -0.77673295 0.50246096
>
> colMeans(tmp2)
[1] -0.08906359
> colSums(tmp2)
[1] -8.906359
> colVars(tmp2)
[1] 1.137425
> colSd(tmp2)
[1] 1.066501
> colMax(tmp2)
[1] 2.579912
> colMin(tmp2)
[1] -2.380263
> colMedians(tmp2)
[1] -0.196049
> colRanges(tmp2)
[,1]
[1,] -2.380263
[2,] 2.579912
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.09768844 -1.96299233 -2.73580764 0.76350064 -0.02005413 3.06150656
[7] -1.54104790 -0.37718345 -2.24956491 -3.06900269
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.2570586
[2,] -0.3430128
[3,] 0.1234225
[4,] 0.7214211
[5,] 1.1180166
>
> rowApply(tmp,sum)
[1] -0.04689026 -3.54194206 -5.55792615 0.76745423 1.26365772 0.10959873
[7] 4.62340696 -1.61131173 -3.30133187 0.26232700
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 5 10 7 9 9 2 4 7 8 4
[2,] 8 5 5 4 1 3 10 6 2 6
[3,] 3 9 10 2 4 9 3 2 3 3
[4,] 1 6 8 10 6 10 5 4 4 5
[5,] 2 1 2 7 2 8 9 8 7 9
[6,] 10 3 6 8 5 6 6 5 5 10
[7,] 6 4 4 3 8 5 8 10 1 2
[8,] 7 7 9 6 3 7 2 1 9 8
[9,] 4 8 3 1 10 4 7 9 6 1
[10,] 9 2 1 5 7 1 1 3 10 7
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -8.618968583 2.261863570 1.826703153 -4.228245274 -2.806540269
[6] -0.004294967 -1.265340484 4.288026094 1.494640404 -0.282538098
[11] -1.206159860 0.993237506 -0.211980923 -3.343255753 -1.369980045
[16] -0.379034278 0.330178899 -0.153570937 1.956187615 -3.417382449
> colApply(tmp,quantile)[,1]
[,1]
[1,] -3.4597507
[2,] -1.9786458
[3,] -1.5723917
[4,] -1.4481202
[5,] -0.1600601
>
> rowApply(tmp,sum)
[1] -11.2428663 -4.2706831 -1.2067904 2.1555516 0.4283335
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 13 1 1 1 4
[2,] 15 19 2 19 9
[3,] 16 12 19 12 14
[4,] 2 2 12 4 13
[5,] 3 13 10 5 7
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.1600601 0.18150994 0.18884639 -1.81282181 -1.53619958 -0.04116085
[2,] -3.4597507 1.51695828 0.02544281 -1.89258744 0.13975053 -0.55490994
[3,] -1.4481202 -1.10154300 0.82629674 0.03544841 -0.09413039 -0.43165914
[4,] -1.9786458 1.59667334 0.35660067 -0.86121214 -0.73318392 -1.15234783
[5,] -1.5723917 0.06826502 0.42951654 0.30292770 -0.58277690 2.17578279
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -1.005742379 1.4834349 -1.0019813 -0.7341728 0.673107648 0.22159512
[2,] -0.748109686 1.5756996 0.7993829 -0.2569307 -1.716679288 0.01398416
[3,] 0.002121672 0.5852281 -0.9864905 0.1709738 -0.423572229 0.79596317
[4,] 0.438089941 -0.2100767 1.1567135 -0.2305317 -0.008541241 -1.31163407
[5,] 0.048299968 0.8537402 1.5270158 0.7681233 0.269525250 1.27332912
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.8679914 -0.9927462 -1.8525311 -1.0481483 0.4028180 -0.8450980
[2,] -0.2233981 -0.4169221 -0.9450565 0.4454880 1.1917810 0.7143822
[3,] -0.5397991 -0.4738642 0.4998950 0.6964199 -0.6913384 1.6724561
[4,] 2.3438173 0.1155194 0.6510433 0.2695298 1.2241924 0.4003446
[5,] -0.9246096 -1.5752426 0.2766693 -0.7423237 -1.7972740 -2.0956559
[,19] [,20]
[1,] -1.1516128 -1.3439116
[2,] 0.5959903 -1.0751985
[3,] 0.3396667 -0.6407428
[4,] 0.7111860 -0.6219852
[5,] 1.4609573 0.2644557
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 655 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 566 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 2.319847 -0.7105746 0.524082 -0.2391194 1.212499 -0.02067971 -0.9830438
col8 col9 col10 col11 col12 col13 col14
row1 1.54064 0.3301902 0.7109543 -0.1841119 0.009539223 1.313253 -1.557477
col15 col16 col17 col18 col19 col20
row1 -0.7336067 -0.6862799 0.6984343 0.514765 -0.1625395 0.2031284
> tmp[,"col10"]
col10
row1 0.7109543
row2 -0.7303839
row3 1.0222081
row4 -0.5905951
row5 -1.9468460
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 2.3198472 -0.7105746 0.524082 -0.23911941 1.2124995 -0.02067971
row5 0.4179617 -0.5432485 -1.363501 0.07785939 -0.8180655 -0.06992854
col7 col8 col9 col10 col11 col12 col13
row1 -0.9830438 1.5406402 0.3301902 0.7109543 -0.1841119 0.009539223 1.313253
row5 0.1015352 0.9718427 -0.1961820 -1.9468460 1.1212055 0.635073098 1.659890
col14 col15 col16 col17 col18 col19
row1 -1.5574769 -0.7336067 -0.68627994 0.6984343 0.514765 -0.1625395
row5 -0.6727939 -0.5210333 -0.03319902 -0.5378556 2.083249 0.7761090
col20
row1 0.2031284
row5 -0.5347638
> tmp[,c("col6","col20")]
col6 col20
row1 -0.02067971 0.20312843
row2 -1.31703347 -0.06705903
row3 1.17800423 2.98637695
row4 -0.01166231 -0.21721967
row5 -0.06992854 -0.53476379
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.02067971 0.2031284
row5 -0.06992854 -0.5347638
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.21367 51.1474 49.89536 49.23687 48.47645 105.1832 51.06187 50.25359
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.37062 49.88094 50.51206 48.61588 49.86175 48.1907 51.39703 50.37924
col17 col18 col19 col20
row1 50.53694 49.49232 49.16116 104.2166
> tmp[,"col10"]
col10
row1 49.88094
row2 30.10439
row3 30.73640
row4 29.83340
row5 49.34480
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.21367 51.14740 49.89536 49.23687 48.47645 105.1832 51.06187 50.25359
row5 49.55368 49.62175 49.53875 49.37184 49.86372 105.2326 51.46828 50.80679
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.37062 49.88094 50.51206 48.61588 49.86175 48.19070 51.39703 50.37924
row5 50.88364 49.34480 50.94393 49.87815 49.47509 49.21651 49.52011 50.26623
col17 col18 col19 col20
row1 50.53694 49.49232 49.16116 104.2166
row5 48.38038 48.47578 48.78226 104.8300
> tmp[,c("col6","col20")]
col6 col20
row1 105.18317 104.21663
row2 75.98440 73.33609
row3 73.21620 74.29035
row4 75.38098 73.99138
row5 105.23256 104.82999
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.1832 104.2166
row5 105.2326 104.8300
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.1832 104.2166
row5 105.2326 104.8300
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 8.978956e-05
[2,] 2.071360e-01
[3,] -1.638283e+00
[4,] -1.173840e+00
[5,] -1.144660e+00
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.1435562 -0.75116260
[2,] -0.6524677 0.52608737
[3,] 0.7698981 -0.19706325
[4,] 1.0221235 0.05575147
[5,] -1.0374724 1.16362822
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.01600127 1.02493249
[2,] -2.36913756 0.80235309
[3,] -0.38659985 -0.24406392
[4,] 1.55658643 0.09237934
[5,] 0.39201409 0.70236882
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.01600127
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.01600127
[2,] -2.36913756
>
>
>
> 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 1.3345083 -0.3651149 0.4667791279 -0.7066976 -1.025634 1.386966 -0.3362108
row1 0.8645458 0.5145948 0.0007570013 -0.3788829 -1.822567 1.085454 1.3781407
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -2.023342 -0.3188303 -0.9376771 -1.5957932 -0.8228005 0.01473718
row1 1.036777 -0.5237400 -1.5099634 -0.4684215 -0.5797430 -1.38039170
[,14] [,15] [,16] [,17] [,18] [,19]
row3 0.7789332 -0.009696693 -2.9696754 0.1162577 0.08900642 0.1014288
row1 -0.9475757 0.189121837 -0.3854953 1.1207964 1.70778537 -0.5185167
[,20]
row3 0.9478192
row1 -1.7006090
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.6444706 0.1144765 -0.07875338 1.861595 1.067454 1.417917 0.383535
[,8] [,9] [,10]
row2 0.9995893 -0.4440974 -0.1411843
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.508318 -0.07465658 0.6619037 -0.5127234 -0.1120743 -0.3698282 1.21574
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.074267 0.6668966 -0.3619737 -0.762824 1.373839 -1.061143 0.335226
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.675924 0.2102988 -0.2937329 -0.221766 -0.4392388 -0.7242103
>
>
> 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: 0x600000f24000>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a363872638"
[2] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a33dde5994"
[3] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a350cb2347"
[4] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a3487933c1"
[5] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a3d34e913"
[6] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a3cb1e52b"
[7] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a3733c708f"
[8] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a3501f764"
[9] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a34418c8cd"
[10] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a337272da8"
[11] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a36d268ce1"
[12] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a37deb3fc2"
[13] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a35fa71a23"
[14] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a353a520e4"
[15] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM159a37e1283a2"
>
>
> ### 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: 0x600000f3c0c0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x600000f3c0c0>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x600000f3c0c0>
> rowMedians(tmp)
[1] -0.275285738 -0.073928720 -0.358634568 -0.315516525 -0.702307910
[6] 0.355917658 0.012105882 -0.056108365 0.308362340 -0.374055084
[11] 0.171348808 -0.090953980 0.230257175 0.066989161 0.247447911
[16] 0.436028711 -0.314672494 -0.324457050 -0.280149394 -0.261965645
[21] -0.281514892 0.112008585 -0.170445660 0.639041246 0.102484824
[26] 0.066033149 -0.722519783 -0.088216580 -0.029739410 0.094845879
[31] -0.105583555 -0.356038532 -0.066574679 -0.107338846 0.062035740
[36] 0.233578864 0.148842550 0.490807070 -0.275917589 -0.249265233
[41] 0.347586005 -0.206486533 -0.179387109 0.347260830 -0.060319800
[46] -0.272195000 0.244876755 -0.007368969 0.010014574 -0.083555953
[51] 0.253275219 0.049978840 0.734496163 0.191578837 0.019076582
[56] 0.162362934 0.237195823 0.084215734 0.644384624 -0.220336531
[61] -0.032929362 -0.547873918 0.174769248 0.203578234 0.299409999
[66] 0.567552080 0.151613015 0.575170043 0.101251584 0.051800275
[71] -0.308130283 -0.607106691 0.347129936 -0.277588311 -0.087428041
[76] 0.696852682 0.461303729 0.120651157 -0.069026693 0.204318610
[81] -0.659412273 -0.503000509 -0.195901791 -0.232193748 0.048309136
[86] -0.074836042 -0.127942694 -0.169993806 0.436778388 0.129999257
[91] 0.290281731 -0.589680881 0.430650935 -0.076394981 0.176107964
[96] 0.036251994 -0.190365466 0.327244969 0.068519927 -0.210725003
[101] -0.326891897 -0.135654172 0.268597696 -0.148551382 -0.174540192
[106] -0.493127588 0.104497520 -0.378738972 -0.041355996 -0.236769768
[111] 0.019076232 0.235301731 0.248933002 0.294257035 0.428599969
[116] -0.438880152 -0.755811524 0.128535699 0.069700582 0.488130903
[121] 0.074682013 0.080744899 -0.222918554 -0.382560221 0.052379361
[126] 0.209478883 -0.407829964 0.615376607 -0.047956639 0.118143152
[131] -0.177661418 -0.694488393 -0.254490221 -0.412723201 0.018663116
[136] -0.579639150 -0.082889184 -0.132247651 -0.548460447 -0.117286124
[141] -0.015189610 0.045296122 -0.393960650 0.025545659 -0.016628176
[146] 0.210390664 -0.710415079 -0.349613247 -0.235391509 0.152192600
[151] -0.297470391 -0.278418301 0.168142384 0.444401895 0.175054419
[156] -0.490270791 -0.505525515 0.420097825 -0.521143818 0.437517395
[161] 0.539328083 0.290535408 0.318431400 0.424444559 -0.426072442
[166] -0.801570516 -0.845110680 -0.101117326 0.224041324 0.433991870
[171] 0.948459416 0.934235611 0.366268097 0.540837567 -0.035915509
[176] -0.028622683 0.142425259 0.503935718 0.177297538 0.119717349
[181] 0.196049542 -0.101781264 -0.258988677 -0.139985663 -0.419044848
[186] 0.163674283 0.257686126 0.229445160 0.126914961 0.053595503
[191] -0.210685858 -0.068666150 0.262840757 0.305019206 -0.781166368
[196] -0.380959746 0.952668377 -0.215812459 -0.088367253 -0.395976462
[201] 0.113835267 0.113574675 0.189885597 -0.307845195 0.050781722
[206] 0.039226306 -0.017809806 0.103915031 0.461823987 0.264745686
[211] -0.493138152 0.153125387 -0.239136993 -0.217389918 0.476303482
[216] 0.286544137 0.281489009 -0.032675875 0.159513590 -0.201892248
[221] -0.333299034 0.169671173 0.585625703 -0.309076508 -0.365896282
[226] -0.281427152 -0.161189024 -0.002030693 -0.028165992 0.438611606
>
> proc.time()
user system elapsed
1.860 10.079 12.282
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003ed4000>
> .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: 0x600003ed4000>
> .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: 0x600003ed4000>
> .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: 0x600003ed4000>
> 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: 0x600003ee8000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003ee8000>
> .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: 0x600003ee8000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003ee8000>
> .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: 0x600003ee8000>
> 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: 0x600003eec000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003eec000>
> .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: 0x600003eec000>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003eec000>
> .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: 0x600003eec000>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600003eec000>
> .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: 0x600003eec000>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600003eec000>
> .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: 0x600003eec000>
> 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: 0x600003eec180>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600003eec180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003eec180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003eec180>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile15d0329b9b620" "BufferedMatrixFile15d035f640446"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile15d0329b9b620" "BufferedMatrixFile15d035f640446"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003eec420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003eec420>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003eec420>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003eec420>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600003eec420>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600003eec420>
> .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: 0x600003eec600>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003eec600>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003eec600>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x600003eec600>
> 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: 0x600003ee0000>
> .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: 0x600003ee0000>
> rm(P)
>
> proc.time()
user system elapsed
0.229 0.096 0.325
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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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
0.237 0.065 0.307