Jonathan Cairns
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/BayesPeak |
| Branch: RELEASE_3_9 |
| Last Commit: b242ddc |
| Last Changed Date: 2019-05-02 11:53:14 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:23:42 -0400 (Wed, 16 Oct 2019).
| Package 113/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BayesPeak 1.36.0 Jonathan Cairns
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: BayesPeak |
| Version: 1.36.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BayesPeak.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BayesPeak_1.36.0.tar.gz |
| StartedAt: 2019-10-16 02:06:10 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:19:51 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 820.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BayesPeak.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BayesPeak.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BayesPeak_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BayesPeak.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BayesPeak/DESCRIPTION' ... OK
* this is package 'BayesPeak' version '1.36.0'
* 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 'BayesPeak' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpegnUHb/R.INSTALL1a6c61f157b1/BayesPeak/man/bayespeak.Rd:72: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpegnUHb/R.INSTALL1a6c61f157b1/BayesPeak/man/bayespeak.Rd:76: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BayesPeak.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 1.0Mb
extdata 5.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'IRanges'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to 'parallel' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
identify.overfitdiag plot.PP plot.bed plot.job plot.overfitdiag
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
identify.overfitdiag: no visible global function definition for
'identify'
plot.job: no visible global function definition for 'plot'
plot.overfitdiag: no visible global function definition for 'plot'
region.overfitdiag: no visible global function definition for 'locator'
region.overfitdiag: no visible global function definition for 'polygon'
Undefined global functions or variables:
identify locator plot polygon
Consider adding
importFrom("graphics", "identify", "locator", "plot", "polygon")
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 ... NOTE
S3 methods shown with full name in documentation object 'overfittingDiagnostics':
'plot.overfitdiag' 'identify.overfitdiag'
S3 methods shown with full name in documentation object 'plot.PP':
'plot.PP'
S3 methods shown with full name in documentation object 'plot.bed':
'plot.bed'
S3 methods shown with full name in documentation object 'plot.job':
'plot.job'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/BayesPeak/libs/i386/BayesPeak.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/BayesPeak/libs/x64/BayesPeak.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 or elapsed time > 5s
user system elapsed
summarise.peaks 186.36 0.03 186.39
bayespeak 173.28 0.03 174.39
plot.job 16.61 0.07 16.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bayespeak 176.42 0.03 176.49
summarise.peaks 165.81 0.00 165.87
plot.job 15.31 0.00 15.37
* 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: 1 WARNING, 7 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/BayesPeak.Rcheck/00check.log'
for details.
BayesPeak.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BayesPeak_1.36.0.tar.gz && rm -rf BayesPeak.buildbin-libdir && mkdir BayesPeak.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BayesPeak.buildbin-libdir BayesPeak_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BayesPeak_1.36.0.zip && rm BayesPeak_1.36.0.tar.gz BayesPeak_1.36.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
22 1693k 22 384k 0 0 1323k 0 0:00:01 --:--:-- 0:00:01 1352k
100 1693k 100 1693k 0 0 5567k 0 --:--:-- --:--:-- --:--:-- 5681k
install for i386
* installing *source* package 'BayesPeak' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c bayespeak.c -o bayespeak.o
bayespeak.c: In function 'bayespeak':
bayespeak.c:176:27: warning: variable 'M' set but not used [-Wunused-but-set-variable]
double M1, M2, M3, M4, M, a, b;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o BayesPeak.dll tmp.def bayespeak.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BayesPeak.buildbin-libdir/00LOCK-BayesPeak/00new/BayesPeak/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BayesPeak'
finding HTML links ... done
bayespeak html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpegnUHb/R.INSTALL1a6c61f157b1/BayesPeak/man/bayespeak.Rd:72: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpegnUHb/R.INSTALL1a6c61f157b1/BayesPeak/man/bayespeak.Rd:76: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
overfitting html
plot.PP html
plot.bed html
plot.job html
raw.output.H3K4me3 html
raw.output html
read.bed html
summarise.peaks 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 'BayesPeak' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c bayespeak.c -o bayespeak.o
bayespeak.c: In function 'bayespeak':
bayespeak.c:176:27: warning: variable 'M' set but not used [-Wunused-but-set-variable]
double M1, M2, M3, M4, M, a, b;
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o BayesPeak.dll tmp.def bayespeak.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BayesPeak.buildbin-libdir/BayesPeak/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BayesPeak' as BayesPeak_1.36.0.zip
* DONE (BayesPeak)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BayesPeak' successfully unpacked and MD5 sums checked
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BayesPeak.Rcheck/examples_i386/BayesPeak-Ex.timings
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BayesPeak.Rcheck/examples_x64/BayesPeak-Ex.timings
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