Mark Pinese
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/messina |
| Branch: RELEASE_3_6 |
| Last Commit: 798d275 |
| Last Changed Date: 2017-10-30 12:40:13 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:24:02 -0400 (Thu, 12 Apr 2018).
| Package 815/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| messina 1.14.0 Mark Pinese
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: messina |
| Version: 1.14.0 |
| Command: rm -rf messina.buildbin-libdir messina.Rcheck && mkdir messina.buildbin-libdir messina.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=messina.buildbin-libdir messina_1.14.0.tar.gz >messina.Rcheck\00install.out 2>&1 && cp messina.Rcheck\00install.out messina-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=messina.buildbin-libdir --install="check:messina-install.out" --force-multiarch --no-vignettes --timings messina_1.14.0.tar.gz |
| StartedAt: 2018-04-12 01:14:57 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:19:46 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 288.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: messina.Rcheck |
| Warnings: 1 |
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### Running command:
###
### rm -rf messina.buildbin-libdir messina.Rcheck && mkdir messina.buildbin-libdir messina.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=messina.buildbin-libdir messina_1.14.0.tar.gz >messina.Rcheck\00install.out 2>&1 && cp messina.Rcheck\00install.out messina-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=messina.buildbin-libdir --install="check:messina-install.out" --force-multiarch --no-vignettes --timings messina_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/messina.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'messina/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'messina' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'messina' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgxypqX/R.INSTALL1f606a4178a1/messina/man/messina.Rd:125: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgxypqX/R.INSTALL1f606a4178a1/messina/man/messinaDE.Rd:130: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgxypqX/R.INSTALL1f606a4178a1/messina/man/messinaSurv.Rd:166: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/messina.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'Biobase' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcBootstrapKaplanMeierEstimatesAtTimes : <anonymous> : <anonymous>:
no visible global function definition for 'approx'
messina: no visible global function definition for 'str'
messinaClassPlot: no visible global function definition for 'reorder'
messinaSurvKMplot : <anonymous>: no visible binding for global variable
'median'
messinaSurvKMplot : <anonymous>: no visible binding for global variable
'quantile'
messinaSurvKMplot : <anonymous>: no visible binding for global variable
'sd'
messinaSurvKMplotSingleGroup: no visible binding for global variable
'median'
messinaSurvKMplotSingleGroup: no visible binding for global variable
'quantile'
messinaSurvKMplotSingleGroup: no visible binding for global variable
'sd'
messinaSurvObjPlot: no visible global function definition for
'quantile'
messinaSurvObjectiveFunc: no visible global function definition for
'coef'
messinaSurvPlot: no visible global function definition for 'str'
Undefined global functions or variables:
approx coef median quantile reorder sd str
Consider adding
importFrom("stats", "approx", "coef", "median", "quantile", "reorder",
"sd")
importFrom("utils", "str")
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-3.6-bioc/meat/messina.buildbin-libdir/messina/libs/i386/messina.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot-MessinaSurvResult-missing-method 43.69 0.08 43.76
messinaSurv 20.78 0.03 20.81
plot-MessinaClassResult-missing-method 8.26 0.02 8.29
messina 6.75 0.08 7.28
messinaTopResults 5.56 0.01 5.57
messinaDE 5.17 0.05 5.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot-MessinaSurvResult-missing-method 46.33 0.08 46.41
messinaSurv 20.21 0.00 20.20
messina 6.79 0.04 6.81
plot-MessinaClassResult-missing-method 5.86 0.00 5.86
messinaDE 5.05 0.04 5.09
* 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, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/messina.Rcheck/00check.log'
for details.
messina.Rcheck/00install.out
install for i386
* installing *source* package 'messina' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c Classifier.cpp -o Classifier.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c Data.cpp -o Data.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c crossval.cpp -o crossval.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c errors.cpp -o errors.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c messinaExtern.cpp -o messinaExtern.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o messina.dll tmp.def Classifier.o Data.o RcppExports.o crossval.o errors.o init.o messinaExtern.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/messina.buildbin-libdir/messina/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'messina'
finding HTML links ... done
MessinaFits-class html
MessinaParameters-class html
MessinaResult-class html
messina-package html
messina html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgxypqX/R.INSTALL1f606a4178a1/messina/man/messina.Rd:125: missing file link 'ExpressionSet'
messinaDE html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgxypqX/R.INSTALL1f606a4178a1/messina/man/messinaDE.Rd:130: missing file link 'ExpressionSet'
messinaSurv html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpgxypqX/R.INSTALL1f606a4178a1/messina/man/messinaSurv.Rd:166: missing file link 'ExpressionSet'
messinaTopResults html
plot-MessinaClassResult-missing-method
html
plot-MessinaSurvResult-missing-method html
show-methods html
tcga_kirc_example html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'messina' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c Classifier.cpp -o Classifier.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c Data.cpp -o Data.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c crossval.cpp -o crossval.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c errors.cpp -o errors.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c messinaExtern.cpp -o messinaExtern.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o messina.dll tmp.def Classifier.o Data.o RcppExports.o crossval.o errors.o init.o messinaExtern.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/messina.buildbin-libdir/messina/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'messina' as messina_1.14.0.zip
* DONE (messina)
In R CMD INSTALL
In R CMD INSTALL
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messina.Rcheck/examples_i386/messina-Ex.timings
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messina.Rcheck/examples_x64/messina-Ex.timings
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