Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-20 15:04:46 -0400 (Mon, 20 Sep 2021).

CHECK results for csaw on nebbiolo1

To the developers/maintainers of the csaw package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/csaw.git to
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raw results

Package 416/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.26.0  (landing page)
Aaron Lun
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/csaw
git_branch: RELEASE_3_13
git_last_commit: d3850f3
git_last_commit_date: 2021-05-19 12:08:51 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: csaw
Version: 1.26.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings csaw_1.26.0.tar.gz
StartedAt: 2021-09-19 09:24:24 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 09:32:26 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 481.6 seconds
RetCode: 0
Status:   OK  
CheckDir: csaw.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings csaw_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/csaw.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘csaw/DESCRIPTION’ ... OK
* this is package ‘csaw’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘csaw’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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 is not available
File ‘/home/biocbuild/bbs-3.13-bioc/R/library/csaw/libs/csaw.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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
detailRanges 13.674   1.18   14.86
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/csaw.Rcheck/00check.log’
for details.



Installation output

csaw.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL csaw
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘csaw’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c annotator.cpp -o annotator.o
annotator.cpp: In function ‘SEXPREC* annotate_overlaps(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
annotator.cpp:47:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   47 |         while (counter < nolaps && query[counter]==curreg) {
      |                ~~~~~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_utils.cpp -o bam_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c best_in_cluster.cpp -o best_in_cluster.o
best_in_cluster.cpp: In function ‘SEXPREC* best_in_cluster(SEXP, SEXP, SEXP)’:
best_in_cluster.cpp:11:10: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   11 |  if (nwin!=clustids.size() || nwin!=winweight.size()) {
      |      ~~~~^~~~~~~~~~~~~~~~~
best_in_cluster.cpp:11:35: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   11 |  if (nwin!=clustids.size() || nwin!=winweight.size()) {
      |                               ~~~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c check_bimodality.cpp -o check_bimodality.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c correlate_reads.cpp -o correlate_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c find_maxima.cpp -o find_maxima.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c get_profile.cpp -o get_profile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c get_rle_counts.cpp -o get_rle_counts.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c intersector.cpp -o intersector.o
intersector.cpp: In constructor ‘intersector::intersector(SEXP, SEXP)’:
intersector.cpp:8:10: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
    8 |     if (N!=elements.size()) {
      |         ~^~~~~~~~~~~~~~~~~
intersector.cpp:32:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
   32 |         if (current < 0 || current >= nelements) {
      |                            ~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c merge_windows.cpp -o merge_windows.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pair_reads.cpp -o pair_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c single_reads.cpp -o single_reads.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_profile.o get_rle_counts.o init.o intersector.o merge_windows.o pair_reads.o single_reads.o utils.o /home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-csaw/00new/csaw/libs
** 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
** 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 (csaw)

Tests output

csaw.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-pc-linux-gnu (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(csaw)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
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("csaw")
[ FAIL 0 | WARN 40 | SKIP 0 | PASS 2696 ]
> 
> 
> proc.time()
   user  system elapsed 
278.383   3.718 282.108 

Example timings

csaw.Rcheck/csaw-Ex.timings

nameusersystemelapsed
SEmethods1.0050.0051.013
calculateCPM0.3990.0000.399
checkBimodality0.6110.0080.619
clusterFDR1.4240.1001.524
clusterWindows3.1000.0243.123
clusterWindowsList4.4450.0394.485
combineTests0.1120.0010.112
correlateReads0.2900.0000.289
csawUsersGuide0.0000.0010.000
defunct0.0000.0010.001
detailRanges13.674 1.18014.860
empiricalFDR0.1880.0000.188
extractReads2.2630.0122.275
filterWindows1.4750.0081.486
findMaxima0.2940.0040.298
getBestTest0.1440.0000.144
getPESizes0.1310.0000.131
getWidths1.1210.0081.130
maximizeCcf0.0010.0010.001
mergeResults0.2520.0070.259
mergeResultsList0.3460.0000.347
mergeWindows0.0980.0000.098
mergeWindowsList1.0360.0001.036
minimalTests0.0220.0000.022
mixedTests0.1180.0000.118
normFactors0.0620.0000.062
normOffsets0.1460.0000.145
overlapStats1.8350.0041.839
profileSites1.1510.0081.159
readParam0.0520.0010.053
regionCounts0.6390.0020.642
scaledAverage0.9060.0200.927
strandedCounts3.8830.0323.915
upweightSummit0.0060.0000.005
windowCounts2.8270.0042.832
wwhm0.1610.0000.161