Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-06 11:05:04 -0500 (Mon, 06 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 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
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 440/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.33.0  (landing page)
Aaron Lun
Snapshot Date: 2023-02-05 14:00:11 -0500 (Sun, 05 Feb 2023)
git_url: https://git.bioconductor.org/packages/csaw
git_branch: master
git_last_commit: 613823d
git_last_commit_date: 2022-11-01 11:10:35 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: csaw
Version: 1.33.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings csaw_1.33.0.tar.gz
StartedAt: 2023-02-05 19:57:55 -0500 (Sun, 05 Feb 2023)
EndedAt: 2023-02-05 20:05:05 -0500 (Sun, 05 Feb 2023)
EllapsedTime: 429.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: csaw.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings csaw_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/csaw.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘csaw/DESCRIPTION’ ... OK
* this is package ‘csaw’ version ‘1.33.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
* 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 ... WARNING
checkRd: (5) readParam.Rd:84-87: \item in \describe must have non-empty label
checkRd: (5) readParam.Rd:94-96: \item in \describe must have non-empty label
checkRd: (5) readParam.Rd:103-105: \item in \describe must have non-empty label
checkRd: (5) readParam.Rd:106-109: \item in \describe must have non-empty label
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/library/csaw/libs/csaw.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (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 nor [v]sprintf. 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 12.834  0.687  13.522
* 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 ...
  ‘csaw.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/csaw.Rcheck/00check.log’
for details.



Installation output

csaw.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL csaw
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘csaw’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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:11:17: 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:11:42: 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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-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-3.17-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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

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, aperm, 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")
[E::sam_itr_next] Null iterator
[ FAIL 0 | WARN 40 | SKIP 0 | PASS 2696 ]

[ FAIL 0 | WARN 40 | SKIP 0 | PASS 2696 ]
> 
> 
> proc.time()
   user  system elapsed 
223.050   3.513 226.561 

Example timings

csaw.Rcheck/csaw-Ex.timings

nameusersystemelapsed
SEmethods0.3170.0270.347
calculateCPM0.2530.0410.294
checkBimodality0.4670.0090.474
clusterFDR0.9500.0000.949
clusterWindows1.9850.0192.005
clusterWindowsList2.6980.0092.706
combineTests0.1190.0040.123
correlateReads0.2320.0120.244
csawUsersGuide000
defunct000
detailRanges12.834 0.68713.522
empiricalFDR0.1950.0040.200
extractReads0.8450.0280.873
filterWindows0.9970.1271.125
findMaxima0.1530.0120.164
getBestTest0.1440.0000.145
getPESizes0.0840.0030.088
getWidths0.5920.0010.592
maximizeCcf0.0010.0000.001
mergeResults0.2230.0000.222
mergeResultsList1.1560.1351.291
mergeWindows0.0460.0040.050
mergeWindowsList0.5280.0110.541
minimalTests0.0260.0000.026
mixedTests0.1000.0070.108
normFactors0.0390.0000.040
normOffsets0.0950.0000.095
overlapStats0.7120.0160.728
profileSites0.7390.0360.775
readParam0.0420.0040.045
regionCounts0.3610.0120.373
scaledAverage0.4900.0240.514
strandedCounts1.9200.0081.928
upweightSummit0.0050.0000.005
windowCounts1.0280.0121.039
wwhm0.1040.0000.103