| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the compcodeR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/compcodeR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 369/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compcodeR 1.28.0 (landing page) Charlotte Soneson
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: compcodeR |
| Version: 1.28.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.28.0.tar.gz |
| StartedAt: 2021-10-14 17:42:19 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:48:49 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 390.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: compcodeR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.28.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/compcodeR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.28.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rpanel’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘compcodeR’ can be installed ... OK
* 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 R 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NBPSeq.createRmd 34.751 1.160 35.933
DESeq2.createRmd 31.528 3.777 35.126
NOISeq.prenorm.createRmd 11.221 8.632 18.810
EBSeq.createRmd 11.248 1.052 12.282
baySeq.createRmd 7.651 1.036 8.608
DSS.createRmd 6.955 1.052 7.956
show-compData-method 5.232 0.840 5.986
convertcompDataToList 5.076 0.813 5.803
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/compcodeR.Rcheck/00check.log’
for details.
compcodeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL compcodeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘compcodeR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (compcodeR)
compcodeR.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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(testthat)
> library(compcodeR)
Loading required package: sm
Package 'sm', version 2.2-5.7: type help(sm) for summary information
>
> test_check("compcodeR")
ordinary text without R code
label: settings (with options)
List of 1
$ echo: logi FALSE
label: modifications (with options)
List of 1
$ echo: logi FALSE
label: calcma (with options)
List of 4
$ echo : logi FALSE
$ dev : chr "png"
$ eval : logi TRUE
$ include: logi TRUE
ordinary text without R code
label: maplot-trueDEstatus (with options)
List of 7
$ echo : logi FALSE
$ dev : chr "png"
$ eval : logi TRUE
$ include: logi TRUE
$ message: logi FALSE
$ error : logi TRUE
$ warning: logi TRUE
ordinary text without R code
label: maplot-nbroutliers (with options)
List of 7
$ echo : logi FALSE
$ dev : chr "png"
$ eval : logi TRUE
$ include: logi TRUE
$ message: logi FALSE
$ error : logi TRUE
$ warning: logi TRUE
ordinary text without R code
label: logfoldchanges (with options)
List of 7
$ echo : logi FALSE
$ dev : chr "png"
$ eval : logi TRUE
$ include: logi TRUE
$ message: logi FALSE
$ error : logi TRUE
$ warning: logi TRUE
[1] "DESeq2.createRmd" "DSS.createRmd"
[3] "EBSeq.createRmd" "NBPSeq.createRmd"
[5] "NOISeq.prenorm.createRmd" "TCC.createRmd"
[7] "baySeq.createRmd" "edgeR.GLM.createRmd"
[9] "edgeR.exact.createRmd" "logcpm.limma.createRmd"
[11] "sqrtcpm.limma.createRmd" "ttest.createRmd"
[13] "voom.limma.createRmd" "voom.ttest.createRmd"
ordinary text without R code
label: unnamed-chunk-1 (with options)
List of 6
$ echo : logi TRUE
$ eval : logi TRUE
$ include: logi TRUE
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An object of class compData
Dataset name: B_625_625
Number of samples: 10
Number of variables: 500
Number of random outliers: 0
Number of single outliers: 0
Number of known truly differentially expressed genes: 50
Differential expression analysis was performed by the method EBSeq.1.32.0.median on Thu Oct 14 17:48:09 2021 .
count.matrix:
sample1 sample2 sample3 sample4 sample5 sample6
g1 4 8 5 2 8 8
g2 314 419 186 172 294 133
g3 1030 1583 1011 1033 747 1291
g4 0 1 1 0 2 2
g5 48 122 215 62 106 90
g6 27 16 18 44 29 74
+ 494 rows and 4 cols...
sample.annotations:
condition depth.factor
sample1 1 1.1049378
sample2 1 1.2875127
sample3 1 1.1581115
sample4 1 1.3611698
sample5 1 1.0581603
sample6 2 0.7594447
+ 4 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.11610054 0.11610054 6.878049 16.363472
g2 0.43796296 0.43796296 303.073171 893.165617
g3 0.04321133 0.04321133 1223.414634 2760.990905
g4 0.55624371 0.55624371 0.902439 6.153083
g5 0.15968189 0.15968189 148.146341 316.915193
g6 0.36378999 0.36378999 40.439024 132.785087
n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
g1 0 0 1.158386 2.9291506
g2 0 0 1.349570 8.6365105
g3 0 0 1.050582 10.4859190
g4 0 0 1.432447 0.7393097
g5 0 0 1.185233 7.1150497
g6 0 0 2.176450 5.6916570
truelog2foldchanges upregulation downregulation differential.expression
g1 1.250408 1 0 1
g2 1.559262 1 0 1
g3 1.174273 1 0 1
g4 2.769408 1 0 1
g5 1.097074 1 0 1
g6 1.715273 1 0 1
+ 494 rows...
Differential expression results:
FDR lfdr score posterior.DE
g1 9.063873e-01 1.000000e+00 0.0936127 3.618046e-19
g2 2.191315e-01 6.800099e-01 0.7808685 3.199901e-01
g3 7.537978e-04 2.194364e-03 0.9992462 9.978056e-01
g4 3.164914e-01 7.574579e-01 0.6835086 2.425421e-01
g5 2.900704e-01 7.294102e-01 0.7099296 2.705898e-01
g6 3.802565e-06 1.288441e-05 0.9999962 9.999871e-01
+ 494 rows...
An object of class compData
Dataset name: B_625_625
Number of samples: 4
Number of variables: 500
Number of random outliers: 0
Number of single outliers: 0
Number of known truly differentially expressed genes: 50
Differential expression analysis was performed by the method EBSeq.1.32.0.median on Thu Oct 14 17:48:09 2021 .
count.matrix:
sample1 sample2 sample3 sample4
g1 4 8 5 2
g2 314 419 186 172
g3 1030 1583 1011 1033
g4 0 1 1 0
g5 48 122 215 62
g6 27 16 18 44
+ 494 rows...
sample.annotations:
condition depth.factor
sample1 1 1.1049378
sample2 1 1.2875127
sample3 1 1.1581115
sample4 1 1.3611698
sample5 1 1.0581603
sample6 2 0.7594447
+ 4 rows...
variable.annotations:
truedispersions.S1 truedispersions.S2 truemeans.S1 truemeans.S2
g1 0.11610054 0.11610054 6.878049 16.363472
g2 0.43796296 0.43796296 303.073171 893.165617
g3 0.04321133 0.04321133 1223.414634 2760.990905
g4 0.55624371 0.55624371 0.902439 6.153083
g5 0.15968189 0.15968189 148.146341 316.915193
g6 0.36378999 0.36378999 40.439024 132.785087
n.random.outliers.up.S1 n.random.outliers.up.S2 n.random.outliers.down.S1
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.random.outliers.down.S2 n.single.outliers.up.S1 n.single.outliers.up.S2
g1 0 0 0
g2 0 0 0
g3 0 0 0
g4 0 0 0
g5 0 0 0
g6 0 0 0
n.single.outliers.down.S1 n.single.outliers.down.S2 M.value A.value
g1 0 0 1.158386 2.9291506
g2 0 0 1.349570 8.6365105
g3 0 0 1.050582 10.4859190
g4 0 0 1.432447 0.7393097
g5 0 0 1.185233 7.1150497
g6 0 0 2.176450 5.6916570
truelog2foldchanges upregulation downregulation differential.expression
g1 1.250408 1 0 1
g2 1.559262 1 0 1
g3 1.174273 1 0 1
g4 2.769408 1 0 1
g5 1.097074 1 0 1
g6 1.715273 1 0 1
+ 494 rows...
Differential expression results:
FDR lfdr score posterior.DE
g1 9.063873e-01 1.000000e+00 0.0936127 3.618046e-19
g2 2.191315e-01 6.800099e-01 0.7808685 3.199901e-01
g3 7.537978e-04 2.194364e-03 0.9992462 9.978056e-01
g4 3.164914e-01 7.574579e-01 0.6835086 2.425421e-01
g5 2.900704e-01 7.294102e-01 0.7099296 2.705898e-01
g6 3.802565e-06 1.288441e-05 0.9999962 9.999871e-01
+ 494 rows...
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 285 ]
>
> proc.time()
user system elapsed
121.188 14.922 134.893
compcodeR.Rcheck/compcodeR-Ex.timings
| name | user | system | elapsed | |
| DESeq2.createRmd | 31.528 | 3.777 | 35.126 | |
| DSS.createRmd | 6.955 | 1.052 | 7.956 | |
| EBSeq.createRmd | 11.248 | 1.052 | 12.282 | |
| NBPSeq.createRmd | 34.751 | 1.160 | 35.933 | |
| NOISeq.prenorm.createRmd | 11.221 | 8.632 | 18.810 | |
| TCC.createRmd | 3.803 | 0.496 | 4.261 | |
| baySeq.createRmd | 7.651 | 1.036 | 8.608 | |
| checkDataObject | 0.434 | 0.083 | 0.509 | |
| checkTableConsistency | 1.679 | 0.210 | 1.874 | |
| check_compData | 0.429 | 0.074 | 0.494 | |
| check_compData_results | 1.021 | 0.143 | 1.151 | |
| compData | 0.003 | 0.000 | 0.004 | |
| convertListTocompData | 0.006 | 0.002 | 0.007 | |
| convertcompDataToList | 5.076 | 0.813 | 5.803 | |
| edgeR.GLM.createRmd | 1.656 | 0.189 | 1.828 | |
| edgeR.exact.createRmd | 1.069 | 0.129 | 1.186 | |
| generateCodeHTMLs | 0.983 | 0.134 | 1.107 | |
| generateSyntheticData | 0.436 | 0.070 | 0.498 | |
| listcreateRmd | 0.013 | 0.001 | 0.013 | |
| logcpm.limma.createRmd | 0.758 | 0.123 | 0.870 | |
| runComparison | 1.555 | 0.198 | 1.737 | |
| runComparisonGUI | 0.001 | 0.000 | 0.001 | |
| runDiffExp | 1.049 | 0.146 | 1.182 | |
| show-compData-method | 5.232 | 0.840 | 5.986 | |
| sqrtcpm.limma.createRmd | 0.769 | 0.126 | 0.883 | |
| summarizeSyntheticDataSet | 0.414 | 0.072 | 0.477 | |
| ttest.createRmd | 0.787 | 0.120 | 0.896 | |
| voom.limma.createRmd | 0.959 | 0.127 | 1.074 | |
| voom.ttest.createRmd | 0.833 | 0.126 | 0.947 | |