Per Broberg,
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/SAGx |
| Branch: RELEASE_3_11 |
| Last Commit: e11022c |
| Last Changed Date: 2020-04-27 14:14:01 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:44 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE SAGx PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1567/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SAGx 1.62.0 Per Broberg,
| 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 | OK | OK | |
| Package: SAGx |
| Version: 1.62.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SAGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SAGx_1.62.0.tar.gz |
| StartedAt: 2020-10-17 07:54:58 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 07:56:36 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 98.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SAGx.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:SAGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SAGx_1.62.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SAGx.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 'SAGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SAGx' version '1.62.0'
* 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 'SAGx' 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' calls to packages already attached by Depends:
'methods' 'stats'
Please remove these calls from your code.
Packages in Depends field not imported from:
'methods' 'multtest'
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
File 'SAGx/R/internal.R':
.onLoad calls:
require(methods)
Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
Fstat: no visible binding for global variable 'M'
GSEA.mean.t: no visible binding for global variable 'samroc.res'
GSEA.mean.t: no visible binding for global variable 'kegg'
GSEA.mean.t : maxmeanf: no visible binding for global variable
'plustat'
R2BASE: no visible binding for global variable 'clingen'
R2BASE: no visible binding for global variable 'AZID'
R2BASE: no visible binding for global variable 'dats'
R2BASE: no visible binding for global variable 'annots'
R2BASE: no visible global function definition for 'write.table'
R2mim: no visible binding for global variable 'inm'
R2mim: no visible global function definition for 'write.table'
Xprep: no visible binding for global variable 'M'
Xprep.resid: no visible binding for global variable 'M'
clin2mim: no visible binding for global variable 'dbs'
clin2mim: no visible binding for global variable 'clinical'
clin2mim: no visible global function definition for 'write.table'
estimatep0: no visible binding for global variable 'pp'
fetchSignal: no visible global function definition for 'sqlQuery'
fp.fn: no visible binding for global variable 'pvals'
gap: no visible binding for global variable 'swiss'
gap: no visible binding for global variable 'g'
list.experiments: no visible global function definition for 'sqlQuery'
mat2TeX: no visible global function definition for 'errif'
myclus: no visible binding for global variable 'swiss'
p0.mom: no visible binding for global variable 'pvalues'
p0.mom: no visible global function definition for 'hist'
pava.fdr: no visible binding for global variable 'pvalues'
rank.genes: no visible binding for global variable 'indats'
rank.trend: no visible binding for global variable 'x'
rsd.test: no visible binding for global variable 'x'
rsd.test: no visible binding for global variable 'y'
samrocN: no visible binding for global variable 'M'
samrocNboot: no visible binding for global variable 'M'
plot,samroc.result-ANY : plot.samroc.result: no visible global function
definition for 'lines'
plot,samroc.result-ANY : plot.samroc.result: no visible global function
definition for 'legend'
Undefined global functions or variables:
AZID M annots clingen clinical dats dbs errif g hist indats inm kegg
legend lines plustat pp pvals pvalues samroc.res sqlQuery swiss
write.table x y
Consider adding
importFrom("datasets", "swiss")
importFrom("graphics", "hist", "legend", "lines")
importFrom("utils", "write.table")
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 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/SAGx/libs/i386/SAGx.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/SAGx/libs/x64/SAGx.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (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 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-3.11-bioc/meat/SAGx.Rcheck/00check.log'
for details.
SAGx.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/SAGx_1.62.0.tar.gz && rm -rf SAGx.buildbin-libdir && mkdir SAGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAGx.buildbin-libdir SAGx_1.62.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SAGx_1.62.0.zip && rm SAGx_1.62.0.tar.gz SAGx_1.62.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 42982 100 42982 0 0 714k 0 --:--:-- --:--:-- --:--:-- 807k
install for i386
* installing *source* package 'SAGx' ...
** 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 minigsea.c -o minigsea.o
minigsea.c: In function 'MiniGSEA':
minigsea.c:8:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
int i,j,k,I;
^
"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 newboot.c -o newboot.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 samrocNboot.c -o samrocNboot.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o SAGx.dll tmp.def minigsea.o newboot.o samrocNboot.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/SAGx.buildbin-libdir/00LOCK-SAGx/00new/SAGx/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SAGx'
finding HTML links ... done
Fstat html
GSEA.mean.t html
JT.test html
R2BASE html
R2mim html
Xprep html
Xprep.resid html
clin2mim html
cluster.q html
estimatep0 html
fetchSignal html
firstpass html
fom html
fp.fn html
gap html
list.experiments html
list.intersection.p html
mat2TeX html
myclus html
normalise html
one.probeset.per.gene html
outlier html
p0.mom html
pava.fdr html
pava html
rank.genes html
rank.trend html
rsd.test html
samroc.result-class html
samrocn html
samrocnboot html
union.of.pways 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 'SAGx' ...
** 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 minigsea.c -o minigsea.o
minigsea.c: In function 'MiniGSEA':
minigsea.c:8:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
int i,j,k,I;
^
"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 newboot.c -o newboot.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 samrocNboot.c -o samrocNboot.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o SAGx.dll tmp.def minigsea.o newboot.o samrocNboot.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/SAGx.buildbin-libdir/SAGx/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SAGx' as SAGx_1.62.0.zip
* DONE (SAGx)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SAGx' successfully unpacked and MD5 sums checked
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SAGx.Rcheck/examples_i386/SAGx-Ex.timings
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SAGx.Rcheck/examples_x64/SAGx-Ex.timings
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