Alexis Delabriere
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/proFIA |
| Branch: RELEASE_3_7 |
| Last Commit: ef65247 |
| Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:43:09 -0400 (Wed, 17 Oct 2018).
| Package 1130/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proFIA 1.6.0 Alexis Delabriere
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: proFIA |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proFIA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings proFIA_1.6.0.tar.gz |
| StartedAt: 2018-10-17 04:04:54 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:14:39 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 585.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proFIA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proFIA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings proFIA_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/proFIA.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'proFIA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'proFIA' version '1.6.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'proFIA' 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 ... 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-3.7-bioc/R/library/proFIA/libs/i386/proFIA.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
Examples with CPU or elapsed time > 5s
user system elapsed
proFIAset 102.61 2.64 105.28
impute.FIA-proFIAset-method 13.25 0.27 13.52
findFIASignal 12.99 0.45 13.44
impute.randomForest-proFIAset-method 11.94 0.14 12.08
estimateNoiseMS 6.47 0.59 7.06
plotFlowgrams-proFIAset-method 6.77 0.12 6.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
proFIAset 93.45 2.00 95.46
impute.FIA-proFIAset-method 16.15 0.08 16.25
impute.randomForest-proFIAset-method 15.57 0.11 15.67
findFIASignal 13.25 0.44 13.69
plotFlowgrams-proFIAset-method 6.37 0.14 6.52
estimateNoiseMS 5.11 0.47 5.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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-3.7-bioc/meat/proFIA.Rcheck/00check.log'
for details.
proFIA.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/proFIA_1.6.0.tar.gz && rm -rf proFIA.buildbin-libdir && mkdir proFIA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proFIA.buildbin-libdir proFIA_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL proFIA_1.6.0.zip && rm proFIA_1.6.0.tar.gz proFIA_1.6.0.zip
###
##############################################################################
##############################################################################
% 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 311k 100 311k 0 0 5029k 0 --:--:-- --:--:-- --:--:-- 5567k
install for i386
* installing *source* package 'proFIA' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c UtilFunc.c -o UtilFunc.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c fastMatchPpm.c -o fastMatchPpm.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o proFIA.dll tmp.def FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/proFIA.buildbin-libdir/proFIA/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'proFIA'
finding HTML links ... done
acquisitionDirectory html
analyzeAcquisitionFIA html
determiningInjectionZone html
determiningSizePeak.Geom html
estimateNoiseMS html
exportDataMatrix-proFIAset-method html
exportExpressionSet-proFIAset-method html
exportPeakTable-proFIAset-method html
exportSampleMetadata-proFIAset-method html
exportVariableMetadata-proFIAset-method
html
findBandsFIA html
findFIASignal html
findMzGroup-proFIAset-method html
getInjectionPeak html
group.FIA-proFIAset-method html
impute.FIA-proFIAset-method html
impute.KNN_TN-proFIAset-method html
impute.randomForest-proFIAset-method html
makeDataMatrix-proFIAset-method html
noiseEstimation-class html
peaksGroup-proFIAset-method html
plot html
plotFlowgrams-proFIAset-method html
plotNoise html
plotRaw-proFIAset-method html
plotSamplePeaks-proFIAset-method html
proFIA-package html
proFIAset-class html
proFIAset html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'proFIA' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c UtilFunc.c -o UtilFunc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c fastMatchPpm.c -o fastMatchPpm.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o proFIA.dll tmp.def FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/proFIA.buildbin-libdir/proFIA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proFIA' as proFIA_1.6.0.zip
* DONE (proFIA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'proFIA' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
proFIA.Rcheck/tests_i386/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("proFIA")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
This is MSnbase version 2.6.4
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
This is xcms version 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Loading required package: plasFIA
A mass interval of 0.0153m/z will be used for the density estimation.
0 :0 10 :29 20 :54 30 :78 30 :105 40 :141 50 :174 60 :196 70 :208 80 :215 90 :219
219 groups have been done .
RUNIT TEST PROTOCOL -- Wed Oct 17 04:14:23 2018
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
proFIA RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
10.73 0.54 11.46
|
proFIA.Rcheck/tests_x64/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("proFIA")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
This is MSnbase version 2.6.4
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
This is xcms version 3.2.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Loading required package: plasFIA
A mass interval of 0.0153m/z will be used for the density estimation.
0 :0 10 :29 20 :54 30 :78 30 :105 40 :141 50 :174 60 :196 70 :208 80 :215 90 :219
219 groups have been done .
RUNIT TEST PROTOCOL -- Wed Oct 17 04:14:34 2018
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
proFIA RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
10.07 0.39 10.64
|
|
proFIA.Rcheck/examples_i386/proFIA-Ex.timings
|
proFIA.Rcheck/examples_x64/proFIA-Ex.timings
|