flagme 1.32.0
Mark Robinson , Riccardo Romoli
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/flagme | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf flagme.buildbin-libdir flagme.Rcheck && mkdir flagme.buildbin-libdir flagme.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flagme.buildbin-libdir flagme_1.32.0.tar.gz >flagme.Rcheck\00install.out 2>&1 && cp flagme.Rcheck\00install.out flagme-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=flagme.buildbin-libdir --install="check:flagme-install.out" --force-multiarch --no-vignettes --timings flagme_1.32.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/flagme.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flagme/DESCRIPTION' ... OK
* this is package 'flagme' version '1.32.0'
* checking package namespace information ... NOTE
Namespace with empty importFrom: 'gcspikelite'
* 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 'flagme' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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-3.5-bioc/meat/flagme.buildbin-libdir/flagme/libs/i386/flagme.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 the system RNG.
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
dynRT 23.16 0.28 23.44
corPrt 22.51 0.58 24.47
ndpRT 22.73 0.21 22.93
peaksAlignment 22.41 0.31 22.72
retFatMatrix 22.37 0.26 22.64
plotSpectra 21.71 0.13 21.84
imputePeaks 10.84 0.07 10.98
plot 9.01 0.14 9.15
calcTimeDiffs 7.25 0.11 9.00
multipleAlignment 6.94 0.04 6.99
rmaFitUnit 6.63 0.07 6.68
addXCMSPeaks 6.17 0.11 6.31
compress 6.03 0.06 6.09
addAMDISPeaks 5.70 0.28 8.36
clusterAlignment 5.77 0.02 5.78
gatherInfo 5.77 0.01 5.78
peaksDataset 5.66 0.08 5.74
progressiveAlignment 5.60 0.03 5.63
normDotProduct 5.19 0.01 5.21
dp 5.14 0.05 5.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
retFatMatrix 29.60 0.23 29.83
dynRT 28.83 0.42 29.25
peaksAlignment 28.31 0.53 28.85
corPrt 28.25 0.50 28.75
ndpRT 27.89 0.43 28.33
plotSpectra 27.08 0.17 27.25
imputePeaks 11.48 0.17 11.66
rmaFitUnit 9.09 0.05 9.14
gatherInfo 8.92 0.08 9.00
plot 8.28 0.08 8.36
multipleAlignment 7.77 0.13 7.89
calcTimeDiffs 7.67 0.12 7.80
addXCMSPeaks 7.39 0.11 7.50
clusterAlignment 7.18 0.06 7.23
dp 6.31 0.14 6.45
progressiveAlignment 6.15 0.03 6.19
compress 6.01 0.13 6.14
addAMDISPeaks 5.93 0.08 6.02
normDotProduct 5.83 0.10 5.92
peaksDataset 5.13 0.11 5.23
* 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-3.5-bioc/meat/flagme.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'flagme' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dp.c -o dp.o
dp.c: In function 'dp':
dp.c:218:21: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
double gap=*gap_, cur_min, a, b, c;
^
dp.c:217:30: warning: 'tb' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i,j, nr=*nr_, nc=*nc_, tb, count=0, done=0;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pearson.c -o pearson.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o flagme.dll tmp.def dp.o init.o pearson.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/flagme.buildbin-libdir/flagme/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'flagme' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dp.c -o dp.o
dp.c: In function 'dp':
dp.c:263:26: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
D[(i+1)+(j+1)*(nr+1)] = cur_min;
^
dp.c:264:28: warning: 'tb' may be used uninitialized in this function [-Wmaybe-uninitialized]
phi[(i+1)+(j+1)*(nr+1)] = tb;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pearson.c -o pearson.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o flagme.dll tmp.def dp.o init.o pearson.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/flagme.buildbin-libdir/flagme/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flagme' as flagme_1.32.0.zip
* DONE (flagme)