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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).

CHECK results for CSAR on nebbiolo1

To the developers/maintainers of the CSAR package:
- Please 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 How and When does the builder pull? When will my changes propagate? here 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 415/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSAR 1.44.0  (landing page)
Jose M Muino
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CSAR
git_branch: RELEASE_3_13
git_last_commit: 3eef45f
git_last_commit_date: 2021-05-19 11:44:30 -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: CSAR
Version: 1.44.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CSAR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CSAR_1.44.0.tar.gz
StartedAt: 2021-10-14 09:26:02 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:28:37 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 154.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CSAR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CSAR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CSAR_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CSAR.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 ‘CSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSAR’ version ‘1.44.0’
* 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 ‘CSAR’ can be installed ... OK
* 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 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
CSAR-package           17.028  0.284  17.313
getThreshold           15.941  0.023  15.984
getPermutatedWinScores 15.003  0.015  15.020
permutatedWinScores    14.787  0.008  14.795
distance2Genes          6.061  0.004   6.065
genesWithPeaks          5.505  0.004   5.510
sigWin                  5.226  0.000   5.226
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CSAR.Rcheck/00check.log’
for details.



Installation output

CSAR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CSAR
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘CSAR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c CSAR.c -o CSAR.o
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o CSAR.so CSAR.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-CSAR/00new/CSAR/libs
** 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
** 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 (CSAR)

Tests output


Example timings

CSAR.Rcheck/CSAR-Ex.timings

nameusersystemelapsed
CSAR-package17.028 0.28417.313
ChIPseqScore4.1210.0044.125
distance2Genes6.0610.0046.065
genesWithPeaks5.5050.0045.510
getPermutatedWinScores15.003 0.01515.020
getThreshold15.941 0.02315.984
loadMappedReads0.0000.0000.001
mappedReads2Nhits1.6780.0031.681
permutatedWinScores14.787 0.00814.795
sampleSEP3_test0.0020.0000.001
score2wig4.8070.0044.812
sigWin5.2260.0005.226