Peter Humburg
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ChIPseqR |
| git_branch: RELEASE_3_13 |
| git_last_commit: d242683 |
| git_last_commit_date: 2021-05-19 11:44:14 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
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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. |
| Package 298/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPseqR 1.46.0 (landing page) Peter Humburg
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ChIPseqR |
| Version: 1.46.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPseqR_1.46.0.tar.gz |
| StartedAt: 2021-10-14 21:00:14 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:05:46 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 332.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPseqR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPseqR_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPseqR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.46.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/ChIPseqR/libs/i386/ChIPseqR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
alignFeature 8.86 3.25 12.11
BindScore 6.02 0.31 6.33
RLEBindScore-class 6.05 0.21 6.25
simpleNucCall 5.64 0.14 5.78
callBindingSites 5.03 0.25 5.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
alignFeature 8.04 2.66 10.70
BindScore 5.41 0.21 5.61
RLEBindScore-class 5.24 0.15 5.39
* 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
'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPseqR.Rcheck/00check.log'
for details.
ChIPseqR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ChIPseqR_1.46.0.tar.gz && rm -rf ChIPseqR.buildbin-libdir && mkdir ChIPseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseqR.buildbin-libdir ChIPseqR_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChIPseqR_1.46.0.zip && rm ChIPseqR_1.46.0.tar.gz ChIPseqR_1.46.0.zip
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100 42594 100 42594 0 0 270k 0 --:--:-- --:--:-- --:--:-- 271k
install for i386
* installing *source* package 'ChIPseqR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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/mingw32/bin/gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPseqR.buildbin-libdir/00LOCK-ChIPseqR/00new/ChIPseqR/libs/i386
** 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
install for x64
* installing *source* package 'ChIPseqR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPseqR' as ChIPseqR_1.46.0.zip
* DONE (ChIPseqR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ChIPseqR' successfully unpacked and MD5 sums checked
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ChIPseqR.Rcheck/examples_i386/ChIPseqR-Ex.timings
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ChIPseqR.Rcheck/examples_x64/ChIPseqR-Ex.timings
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