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This page was generated on 2022-06-24 12:05:53 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for DESeq2 on palomino3


To the developers/maintainers of the DESeq2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DESeq2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 514/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESeq2 1.36.0  (landing page)
Michael Love
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/DESeq2
git_branch: RELEASE_3_15
git_last_commit: 2800b78
git_last_commit_date: 2022-04-26 11:13:44 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DESeq2
Version: 1.36.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DESeq2.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DESeq2_1.36.0.tar.gz
StartedAt: 2022-06-24 00:25:40 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 00:34:04 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 504.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DESeq2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DESeq2.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DESeq2_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/DESeq2.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DESeq2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DESeq2' version '1.36.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DESeq2' 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/DESeq2/libs/x64/DESeq2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
results 8.25   0.08    8.33
DESeq   5.59   0.19    5.80
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/DESeq2.Rcheck/00check.log'
for details.



Installation output

DESeq2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DESeq2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DESeq2' ...
** using staged installation
** libs
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c DESeq2.cpp -o DESeq2.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -s -static-libgcc -o DESeq2.dll tmp.def DESeq2.o RcppExports.o -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-DESeq2/00new/DESeq2/libs/x64
** 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 (DESeq2)

Tests output

DESeq2.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("DESeq2")

warning: solve(): system is singular (rcond: 2.4542e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.1485e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.60856e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.04428e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.00017e-16); attempting approx solution

warning: solve(): system is singular (rcond: 2.11853e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.38737e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.4018e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.42504e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.45356e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.32062e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.47034e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.38737e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.4018e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.42504e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.45356e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.32062e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.47034e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.38737e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.4018e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.42504e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.45356e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.32062e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.47034e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.38737e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.4018e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.42504e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.45356e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.32062e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.47034e-17); attempting approx solution
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 231 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 231 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 215.53    4.79  223.96 

Example timings

DESeq2.Rcheck/DESeq2-Ex.timings

nameusersystemelapsed
DESeq5.590.195.80
DESeqDataSet0.170.000.17
coef3.340.033.38
collapseReplicates0.380.000.37
counts0.30.00.3
design0.150.000.15
dispersionFunction1.750.031.79
estimateDispersions1.190.001.19
estimateDispersionsGeneEst1.090.011.11
estimateSizeFactors0.800.040.83
estimateSizeFactorsForMatrix0.240.000.23
fpkm0.720.010.74
fpm0.530.000.53
integrateWithSingleCell000
lfcShrink3.030.093.12
makeExampleDESeqDataSet0.190.000.19
nbinomLRT1.710.041.75
nbinomWaldTest1.640.041.69
normalizationFactors1.930.001.92
plotCounts0.400.000.41
plotDispEsts1.070.021.07
plotMA2.030.032.07
plotPCA1.730.001.73
plotSparsity0.310.000.31
results8.250.088.33
rlog0.970.000.97
summary2.420.002.42
unmix0.440.000.44
varianceStabilizingTransformation0.950.000.95
vst0.910.000.91