Kamal Kishore
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/methylPipe |
| git_branch: RELEASE_3_13 |
| git_last_commit: ca8dade |
| git_last_commit_date: 2021-05-19 12:07:06 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:11 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the methylPipe package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylPipe.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 1112/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylPipe 1.26.0 (landing page) Kamal Kishore
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: methylPipe |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylPipe.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings methylPipe_1.26.0.tar.gz |
| StartedAt: 2021-10-15 01:47:29 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:57:56 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 627.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methylPipe.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylPipe.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings methylPipe_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/methylPipe.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 'methylPipe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylPipe' version '1.26.0'
* 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 'methylPipe' 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
findDMR,BSdataSet: no visible global function definition for
'stopCluster'
findPMDs,BSdata : PMDchr: no visible global function definition for
'segmentPMDs'
methstats,BSdataSet: no visible global function definition for
'stopCluster'
show,BSdata: no visible global function definition for 'organism'
show,BSdataSet: no visible global function definition for 'organism'
Undefined global functions or variables:
organism segmentPMDs stopCluster
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'BSdataSet,ANY,ANY,ANY'
generic '[' and siglist 'GElist,ANY,ANY,ANY'
generic '[[<-' and siglist 'BSdataSet,ANY,ANY,ANY'
generic '[[<-' and siglist 'GElist,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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/methylPipe/libs/i386/methylPipe.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/methylPipe/libs/x64/methylPipe.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' ... WARNING
Found the following significant warnings:
Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpgpPWKO', resetting
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotMeth 24.12 0.58 28.86
findDMR 1.10 3.39 28.03
methstats 1.40 0.42 20.17
findPMDs 0.25 0.36 19.05
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmpec2q1I', resetting
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotMeth 26.09 0.47 30.19
findDMR 0.97 4.45 32.73
methstats 1.19 0.25 21.11
findPMDs 0.26 0.30 19.21
* 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: 3 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/methylPipe.Rcheck/00check.log'
for details.
methylPipe.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/methylPipe_1.26.0.tar.gz && rm -rf methylPipe.buildbin-libdir && mkdir methylPipe.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylPipe.buildbin-libdir methylPipe_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL methylPipe_1.26.0.zip && rm methylPipe_1.26.0.tar.gz methylPipe_1.26.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 397k 100 397k 0 0 1260k 0 --:--:-- --:--:-- --:--:-- 1266k
install for i386
* installing *source* package 'methylPipe' ...
** 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 R_init_methylPipe.c -o R_init_methylPipe.o
"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 binning.c -o binning.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o methylPipe.dll tmp.def R_init_methylPipe.o binning.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/methylPipe.buildbin-libdir/00LOCK-methylPipe/00new/methylPipe/libs/i386
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'methylPipe'
finding HTML links ... done
BSdata-class html
finding level-2 HTML links ... done
BSdataSet-class html
BSprepare html
GEcollection-class html
GElist-class html
chiCombP html
consolidateDMRs html
extractBinGRanges html
findDMR html
findPMDs html
getCpos html
getCposDensity html
mCsmoothing html
mapBSdata2GRanges html
meth.call html
methstats html
methylPipe-package html
plotMeth html
pool.reads html
process.hmc html
profileDNAmetBin html
splitChrs html
tabixdata2GR 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 'methylPipe' ...
** 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 R_init_methylPipe.c -o R_init_methylPipe.o
"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 binning.c -o binning.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o methylPipe.dll tmp.def R_init_methylPipe.o binning.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/methylPipe.buildbin-libdir/methylPipe/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylPipe' as methylPipe_1.26.0.zip
* DONE (methylPipe)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'methylPipe' successfully unpacked and MD5 sums checked
|
methylPipe.Rcheck/examples_i386/methylPipe-Ex.timings
|
methylPipe.Rcheck/examples_x64/methylPipe-Ex.timings
|