Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-27 11:06:56 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 ChIPseqR on riesling1


To the developers/maintainers of the ChIPseqR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPseqR.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 303/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.49.0  (landing page)
Peter Humburg
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/ChIPseqR
git_branch: master
git_last_commit: 853ba4f
git_last_commit_date: 2021-10-26 11:54:55 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPseqR
Version: 1.49.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPseqR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPseqR_1.49.0.tar.gz
StartedAt: 2022-01-26 18:31:05 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 18:34:26 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 200.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPseqR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPseqR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPseqR_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ChIPseqR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' version '1.49.0'
* 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 'ChIPseqR' 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
.fixCounts: no visible global function definition for 'runLength'
.fixCounts: no visible global function definition for 'runValue'
getBindLen: no visible global function definition for 'window'
pickPeak: no visible global function definition for 'start'
pickPeak: no visible global function definition for 'runLength'
pickPeak : <anonymous>: no visible global function definition for
  'window'
[[,BindScore-ANY-numeric: no visible global function definition for
  'window'
decompress,Rle: no visible global function definition for 'runValue'
decompress,RleList : <anonymous>: no visible global function definition
  for 'runValue'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'Rle'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'runValue'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'runValue<-'
plot,RLEReadCounts-missing : <anonymous>: no visible global function
  definition for 'window'
Undefined global functions or variables:
  Rle runLength runValue runValue<- start window
Consider adding
  importFrom("stats", "start", "window")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/ChIPseqR/libs/x64/ChIPseqR.dll':
  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. 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
alignFeature       6.58   8.31   14.89
BindScore          5.30   0.47    5.76
simpleNucCall      5.17   0.45    5.63
RLEBindScore-class 4.69   0.50    5.19
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/ChIPseqR.Rcheck/00check.log'
for details.



Installation output

ChIPseqR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChIPseqR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ChIPseqR' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
  double stat, tmp_stat;
               ^~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ChIPseqR/00new/ChIPseqR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChIPseqR'
    finding HTML links ... done
    BindScore                               html  
    ChIPseqR-package                        html  
    RLEBindScore-class                      html  
    finding level-2 HTML links ... done

    RLEReadCounts-class                     html  
    ReadCounts                              html  
    accessors                               html  
    alignFeature                            html  
    callBindingSites                        html  
    compress-BindScore                      html  
    compress-ReadCounts                     html  
    compress-methods                        html  
    decompress-methods                      html  
    decompress                              html  
    exportBindSequence                      html  
    getBindCor                              html  
    getBindLen                              html  
    getCutoff                               html  
    internal                                html  
    pickPeak                                html  
    plot-BindScore                          html  
    plot-ReadCounts                         html  
    plotReads                               html  
    plotWindow                              html  
    pos2gff                                 html  
    simpleNucCall                           html  
    startScore                              html  
    strandPileup                            html  
    windowCounts                            html  
** 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 (ChIPseqR)
Making 'packages.html' ... done

Tests output


Example timings

ChIPseqR.Rcheck/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore5.300.475.76
ChIPseqR-package000
RLEBindScore-class4.690.505.19
RLEReadCounts-class0.020.000.01
ReadCounts0.010.000.02
alignFeature 6.58 8.3114.89
callBindingSites3.970.424.39
pos2gff000
simpleNucCall5.170.455.63
strandPileup0.020.000.01
windowCounts0.180.000.19