David Rossell
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/gaga |
| Branch: RELEASE_3_11 |
| Last Commit: 014dd85 |
| Last Changed Date: 2020-04-27 14:16:16 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:37 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE gaga PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 648/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gaga 2.34.0 David Rossell
| malbec2 | Linux (Ubuntu 18.04.4 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 | WARNINGS | OK | |
| Package: gaga |
| Version: 2.34.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaga.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gaga_2.34.0.tar.gz |
| StartedAt: 2020-10-17 04:12:12 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:13:47 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 95.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gaga.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaga.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gaga_2.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/gaga.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gaga/DESCRIPTION' ... OK
* this is package 'gaga' version '2.34.0'
* 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 'gaga' 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
adjustfitNN: no visible global function definition for 'predict'
checkfit.gagafit: no visible global function definition for 'is'
checkfit.gagafit: no visible global function definition for 'density'
checkfit.gagafit: no visible global function definition for 'lines'
checkfit.gagafit: no visible global function definition for 'legend'
checkfit.gagafit: no visible global function definition for 'quantile'
checkfit.gagafit: no visible global function definition for 'points'
classpred.gagafit: no visible global function definition for 'is'
findgenes.gagafit: no visible global function definition for 'is'
findgenes.gagafit: no visible global function definition for 'kmeans'
fitGG: no visible global function definition for 'is'
fitGG: no visible global function definition for 'quantile'
fitGG: no visible global function definition for 'var'
fitGG: no visible global function definition for 'kmeans'
fitNN: no visible global function definition for 'is'
fitNNSingleHyp: no visible global function definition for 'is'
forwsimDiffExpr.gagafit: no visible global function definition for 'is'
forwsimDiffExpr.nnfit: no visible global function definition for 'is'
forwsimDiffExpr.nnfit: no visible global function definition for
'quantile'
makeEBarraysSingleHyp: no visible global function definition for 'new'
parest.gagafit: no visible global function definition for 'is'
parest.gagafit: no visible binding for global variable 'quantile'
parest.gagafit: no visible global function definition for 'quantile'
plotForwSim: no visible global function definition for 'lines'
posmeansGG.gagafit: no visible global function definition for 'is'
powclasspred.gagafit: no visible global function definition for 'is'
powfindgenes.gagafit: no visible global function definition for 'is'
powfindgenes.nnfit: no visible global function definition for 'is'
powfindgenes.nnfit: no visible global function definition for 'sd'
powsimprior.nnfit: no visible global function definition for 'sd'
ppGG: no visible global function definition for 'is'
sigmaPriorEst: no visible global function definition for 'is'
sigmaPriorEst: no visible binding for global variable 'var'
sigmaPriorEst: no visible global function definition for 'var'
simGG: no visible global function definition for 'rgamma'
simGG: no visible global function definition for 'new'
simNN: no visible global function definition for 'runif'
simNN: no visible global function definition for 'rnorm'
simNN: no visible global function definition for 'rgamma'
simNN: no visible global function definition for 'new'
simnewsamples.gagafit: no visible global function definition for 'is'
simnewsamples.gagafit: no visible global function definition for 'new'
simnewsamples.nnfit: no visible global function definition for 'is'
simnewsamples.nnfit: no visible global function definition for 'runif'
simnewsamples.nnfit: no visible global function definition for 'rgamma'
simnewsamples.nnfit: no visible global function definition for 'rnorm'
simnewsamples.nnfit: no visible global function definition for
'model.matrix'
simnewsamples.nnfit: no visible global function definition for 'new'
Undefined global functions or variables:
density is kmeans legend lines model.matrix new points predict
quantile rgamma rnorm runif sd var
Consider adding
importFrom("graphics", "legend", "lines", "points")
importFrom("methods", "is", "new")
importFrom("stats", "density", "kmeans", "model.matrix", "predict",
"quantile", "rgamma", "rnorm", "runif", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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-3.11-bioc/R/library/gaga/libs/i386/gaga.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/gaga/libs/x64/gaga.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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/gaga.Rcheck/00check.log'
for details.
gaga.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/gaga_2.34.0.tar.gz && rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gaga.buildbin-libdir gaga_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL gaga_2.34.0.zip && rm gaga_2.34.0.tar.gz gaga_2.34.0.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
0 126k 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
100 126k 100 126k 0 0 113k 0 0:00:01 0:00:01 --:--:-- 114k
install for i386
* installing *source* package 'gaga' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cseqdesma.c -o cseqdesma.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cstat.c -o cstat.o
cstat.c:22:19: warning: 'css_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
^~~~~~~~~~~~~
cstat.c:21:19: warning: 'vector_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char vector_c_sccs_id[] = "%W%";
^~~~~~~~~~~~~~~~
cstat.c:20:19: warning: 'nrutil_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char nrutil_c_sccs_id[] = "%W%";
^~~~~~~~~~~~~~~~
cstat.c:19:19: warning: 'mess_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char mess_c_sccs_id[] = "%W%";
^~~~~~~~~~~~~~
cstat.c:18:19: warning: 'interface_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char interface_c_sccs_id[] = "%W%";
^~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o gaga.dll tmp.def cseqdesma.o cstat.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/gaga.buildbin-libdir/00LOCK-gaga/00new/gaga/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gaga'
finding HTML links ... done
buildPatterns html
checkfit html
classpred html
dcgamma html
findgenes html
fitGG html
forwsimDiffExpr html
geneclus html
getpar html
parest html
plotForwSim html
posmeansGG html
powclasspred html
powfindgenes html
print.gagaclus html
print.gagafit html
print.gagahyp html
seqBoundariesGrid html
simGG html
simnewsamples 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 'gaga' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cseqdesma.c -o cseqdesma.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cstat.c -o cstat.o
cstat.c:22:19: warning: 'css_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
^~~~~~~~~~~~~
cstat.c:21:19: warning: 'vector_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char vector_c_sccs_id[] = "%W%";
^~~~~~~~~~~~~~~~
cstat.c:20:19: warning: 'nrutil_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char nrutil_c_sccs_id[] = "%W%";
^~~~~~~~~~~~~~~~
cstat.c:19:19: warning: 'mess_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char mess_c_sccs_id[] = "%W%";
^~~~~~~~~~~~~~
cstat.c:18:19: warning: 'interface_c_sccs_id' defined but not used [-Wunused-const-variable=]
static const char interface_c_sccs_id[] = "%W%";
^~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o gaga.dll tmp.def cseqdesma.o cstat.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/gaga.buildbin-libdir/gaga/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gaga' as gaga_2.34.0.zip
* DONE (gaga)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'gaga' successfully unpacked and MD5 sums checked
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gaga.Rcheck/examples_i386/gaga-Ex.timings
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gaga.Rcheck/examples_x64/gaga-Ex.timings
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