Hugo Varet
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/rfPred |
| Branch: RELEASE_3_8 |
| Last Commit: 73789cf |
| Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:04 -0400 (Sat, 13 Apr 2019).
| Package 1295/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rfPred 1.20.0 Hugo Varet
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: rfPred |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rfPred.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rfPred_1.20.0.tar.gz |
| StartedAt: 2019-04-13 04:59:21 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:02:23 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 182.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rfPred.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rfPred.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rfPred_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/rfPred.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rfPred/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rfPred' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'rfPred' 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 ... NOTE
'library' or 'require' call to 'Rsamtools' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'IRanges' 'Rsamtools' 'data.table' 'methods' 'parallel'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rfPred_scores_motor: no visible global function definition for
'as.data.table'
rfPred_scores_motor: no visible global function definition for
'IRanges'
rfPred_scores_motor: no visible global function definition for
'scanTabix'
rfPred_scores_motor: no visible global function definition for
'TabixFile'
rfPred_scores_motor: no visible global function definition for
'makeCluster'
rfPred_scores_motor: no visible global function definition for
'parLapply'
rfPred_scores_motor: no visible global function definition for
'clusterSplit'
rfPred_scores_motor : <anonymous>: no visible global function
definition for 'scanTabix'
rfPred_scores_motor: no visible global function definition for
'stopCluster'
rfPred_scores_motor: no visible global function definition for
'write.csv2'
rfPred_scores,GRanges: no visible global function definition for
'seqlevels<-'
rfPred_scores,GRanges: no visible global function definition for
'seqlevels'
rfPred_scores,character: no visible global function definition for
'read.table'
Undefined global functions or variables:
IRanges TabixFile as.data.table clusterSplit makeCluster parLapply
read.table scanTabix seqlevels seqlevels<- stopCluster write.csv2
Consider adding
importFrom("utils", "read.table", "write.csv2")
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 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-3.8-bioc/R/library/rfPred/libs/i386/rfPred.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
** running examples for arch 'x64' ... OK
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/rfPred.Rcheck/00check.log'
for details.
rfPred.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/rfPred_1.20.0.tar.gz && rm -rf rfPred.buildbin-libdir && mkdir rfPred.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rfPred.buildbin-libdir rfPred_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rfPred_1.20.0.zip && rm rfPred_1.20.0.tar.gz rfPred_1.20.0.zip
###
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install for i386
* installing *source* package 'rfPred' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c outstring.c -o outstring.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o rfPred.dll tmp.def outstring.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/rfPred.buildbin-libdir/rfPred/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rfPred'
finding HTML links ... done
example_GRanges html
rfPred-package html
rfPred_scores-methods html
rfPred_scores_motor html
variant_list_Y html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'rfPred' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c outstring.c -o outstring.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o rfPred.dll tmp.def outstring.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/rfPred.buildbin-libdir/rfPred/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rfPred' as rfPred_1.20.0.zip
* DONE (rfPred)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'rfPred' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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rfPred.Rcheck/examples_i386/rfPred-Ex.timings
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rfPred.Rcheck/examples_x64/rfPred-Ex.timings
|