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This page was generated on 2025-08-09 12:06 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 472/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSAR 1.61.1  (landing page)
Jose M Muino
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/CSAR
git_branch: devel
git_last_commit: 6b5b524
git_last_commit_date: 2025-07-24 18:27:20 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CSAR on palomino8

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

raw results


Summary

Package: CSAR
Version: 1.61.1
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CSAR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings CSAR_1.61.1.tar.gz
StartedAt: 2025-08-09 00:58:52 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 01:01:48 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 175.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CSAR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CSAR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings CSAR_1.61.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/CSAR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CSAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CSAR' version '1.61.1'
* 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 'CSAR' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* 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 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 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 ... NOTE
mappedReads2Nhits: no visible global function definition for
  'chromosome'
mappedReads2Nhits: no visible global function definition for 'position'
Undefined global functions or variables:
  chromosome position
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/CSAR/libs/x64/CSAR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
CSAR-package           15.64   0.11   15.78
getThreshold           15.72   0.03   15.75
permutatedWinScores    14.31   0.03   14.34
getPermutatedWinScores 14.04   0.05   14.11
distance2Genes          5.26   0.00    5.28
genesWithPeaks          5.18   0.02    5.19
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/CSAR.Rcheck/00check.log'
for details.


Installation output

CSAR.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL CSAR
###
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'CSAR' ...
** this is package 'CSAR' version '1.61.1'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c CSAR.c -o CSAR.o
gcc -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-CSAR/00new/CSAR/libs/x64
** R
** data
*** moving datasets to lazyload DB
** 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 (CSAR)

Tests output


Example timings

CSAR.Rcheck/CSAR-Ex.timings

nameusersystemelapsed
CSAR-package15.64 0.1115.78
ChIPseqScore4.140.004.17
distance2Genes5.260.005.28
genesWithPeaks5.180.025.19
getPermutatedWinScores14.04 0.0514.11
getThreshold15.72 0.0315.75
loadMappedReads000
mappedReads2Nhits1.610.001.61
permutatedWinScores14.31 0.0314.34
sampleSEP3_test0.000.010.02
score2wig4.190.024.20
sigWin4.930.004.94