Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (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 467/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.40.0  (landing page)
Aaron Lun
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/csaw
git_branch: RELEASE_3_20
git_last_commit: 34ea0d2
git_last_commit_date: 2024-10-29 09:56:01 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for csaw on kunpeng2

To the developers/maintainers of the csaw package:
- 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 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: csaw
Version: 1.40.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings csaw_1.40.0.tar.gz
StartedAt: 2024-11-20 06:43:58 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 06:55:19 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 681.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: csaw.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:csaw.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings csaw_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/csaw.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘csaw/DESCRIPTION’ ... OK
* this is package ‘csaw’ version ‘1.40.0’
* 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++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
* 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 loading without being on the library search path ... 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4.1/site-library/csaw/libs/csaw.so’:
  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 17.74  0.597   20.29
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/csaw.Rcheck/00check.log’
for details.


Installation output

csaw.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL csaw
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘csaw’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.1/site-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/R/R-4.4.1/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/R/R-4.4.1/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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 38 | SKIP 0 | PASS 2695 ]

[ FAIL 0 | WARN 38 | SKIP 0 | PASS 2695 ]
> 
> 
> proc.time()
   user  system elapsed 
389.460   4.380 394.977 

Example timings

csaw.Rcheck/csaw-Ex.timings

nameusersystemelapsed
SEmethods0.5200.0160.543
calculateCPM1.2850.0441.332
checkBimodality0.6150.0320.650
clusterFDR1.4240.0641.491
clusterWindows3.1120.0683.187
clusterWindowsList4.4020.0164.426
combineTests0.1530.0040.157
correlateReads0.3460.0040.351
csawUsersGuide0.0000.0000.001
defunct0.0000.0000.001
detailRanges17.740 0.59720.290
empiricalFDR0.1420.0000.142
extractReads1.1950.0001.199
filterWindows1.3080.0441.356
findMaxima0.2620.0120.274
getBestTest0.2270.0120.240
getPESizes0.1490.0200.169
getWidths0.9010.1401.043
maximizeCcf000
mergeResults0.2640.1080.373
mergeResultsList0.3730.0000.373
mergeWindows0.0850.0000.086
mergeWindowsList0.8090.0080.819
minimalTests0.0370.0000.037
mixedTests0.1680.0080.176
normFactors0.0580.0000.058
normOffsets0.1290.0000.129
overlapStats0.9130.0911.014
profileSites1.1280.0601.191
readParam0.0700.0000.071
regionCounts0.5600.0120.573
scaledAverage0.7600.0240.785
strandedCounts3.1210.1643.293
upweightSummit0.0060.0000.007
windowCounts1.6450.0241.672
wwhm0.1520.0000.153