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This page was generated on 2025-03-17 11:37 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 469/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSAR 1.59.0  (landing page)
Jose M Muino
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/CSAR
git_branch: devel
git_last_commit: 43ca1bc
git_last_commit_date: 2024-10-29 09:32:55 -0400 (Tue, 29 Oct 2024)
palomino7Windows 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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CSAR on palomino7

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: 1.59.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CSAR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings CSAR_1.59.0.tar.gz
StartedAt: 2025-03-17 00:08:01 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 00:10:50 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 169.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CSAR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CSAR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings CSAR_1.59.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/CSAR.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.59.0'
* 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 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
* 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           15.49   0.02   15.51
getThreshold           15.33   0.03   15.37
permutatedWinScores    13.91   0.02   13.94
getPermutatedWinScores 13.70   0.09   13.80
distance2Genes          5.12   0.00    5.89
genesWithPeaks          5.00   0.00    5.47
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/CSAR.Rcheck/00check.log'
for details.


Installation output

CSAR.Rcheck/00install.out

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL CSAR
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'CSAR' ...
** this is package 'CSAR' version '1.59.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"E:/biocbuild/bbs-3.21-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 -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-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-package15.49 0.0215.51
ChIPseqScore3.930.003.94
distance2Genes5.120.005.89
genesWithPeaks5.000.005.47
getPermutatedWinScores13.70 0.0913.80
getThreshold15.33 0.0315.37
loadMappedReads000
mappedReads2Nhits1.660.021.67
permutatedWinScores13.91 0.0213.94
sampleSEP3_test000
score2wig4.330.034.36
sigWin4.770.004.77