Mark Robinson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/flagme |
| Branch: RELEASE_3_9 |
| Last Commit: 2034f83 |
| Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:22:16 -0400 (Wed, 16 Oct 2019).
| Package 553/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flagme 1.40.0 Mark Robinson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: flagme |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flagme.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flagme_1.40.0.tar.gz |
| StartedAt: 2019-10-16 03:42:13 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:57:06 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 892.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flagme.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flagme_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/flagme.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.40.0'
* 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
* 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 ... OK
* checking Rd files ... WARNING
man/plotMultipleSpectra.Rd: non-ASCII input and no declared encoding
problem found in 'plotMultipleSpectra.Rd'
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.9-bioc/R/library/flagme/libs/i386/flagme.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/flagme/libs/x64/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 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
plotMultipleSpectra 39.94 0.77 41.24
corPrt 33.70 0.61 35.50
plotSpectra 31.18 0.53 31.72
ndpRT 29.89 0.75 30.64
peaksAlignment 27.53 0.73 28.26
dynRT 26.08 1.05 27.13
retFatMatrix 14.51 0.11 14.62
imputePeaks 8.53 0.14 8.80
addXCMSPeaks 7.78 0.06 7.86
calcTimeDiffs 7.21 0.10 8.69
multipleAlignment 6.81 0.11 6.95
normDotProduct 6.66 0.08 6.73
plot 6.52 0.22 6.74
progressiveAlignment 6.21 0.05 6.25
compress 5.08 0.20 5.29
clusterAlignment 4.95 0.09 5.04
addAMDISPeaks 4.35 0.18 5.93
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotMultipleSpectra 48.11 0.87 48.99
plotSpectra 39.14 0.55 39.70
peaksAlignment 37.14 0.64 37.78
ndpRT 33.47 0.30 33.76
corPrt 30.78 0.47 31.25
dynRT 29.00 0.36 29.36
retFatMatrix 21.12 0.29 21.41
plot 9.39 0.17 9.56
addXCMSPeaks 9.26 0.14 9.41
progressiveAlignment 8.14 0.06 8.20
rmaFitUnit 8.14 0.01 8.16
imputePeaks 8.09 0.03 8.13
clusterAlignment 5.97 0.09 6.07
compress 5.75 0.08 5.82
calcTimeDiffs 5.53 0.13 5.65
multipleAlignment 5.56 0.05 5.61
normDotProduct 5.42 0.12 5.55
gatherInfo 5.13 0.05 5.17
* 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 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/flagme.Rcheck/00check.log'
for details.
flagme.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/flagme_1.40.0.tar.gz && rm -rf flagme.buildbin-libdir && mkdir flagme.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flagme.buildbin-libdir flagme_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL flagme_1.40.0.zip && rm flagme_1.40.0.tar.gz flagme_1.40.0.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
100 402k 100 402k 0 0 5687k 0 --:--:-- --:--:-- --:--:-- 6288k
install for i386
* installing *source* package 'flagme' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/flagme.buildbin-libdir/00LOCK-flagme/00new/flagme/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flagme'
finding HTML links ... done
addAMDISPeaks html
addChromaTOFPeaks html
addXCMSPeaks html
finding level-2 HTML links ... done
betweenAlignment html
calcTimeDiffs html
clusterAlignment html
compress html
corPrt html
dp html
dynRT html
eitherMatrix html
exportSpectra html
gatherInfo html
imputePeaks html
multipleAlignment html
ndpRT html
normDotProduct html
parseChromaTOF html
parseELU html
peaksAlignment html
peaksDataset html
plot html
plotImage html
plotMultipleSpectra html
plotSpectra html
progressiveAlignment html
retFatMatrix html
rmaFitUnit html
** building package indices
** installing vignettes
'flagme.Rnw' using 'UTF-8'
** 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 'flagme' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/flagme.buildbin-libdir/flagme/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flagme' as flagme_1.40.0.zip
* DONE (flagme)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'flagme' successfully unpacked and MD5 sums checked
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flagme.Rcheck/examples_i386/flagme-Ex.timings
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flagme.Rcheck/examples_x64/flagme-Ex.timings
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