Kornel Labun
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ORFik |
| Branch: RELEASE_3_8 |
| Last Commit: 2e3a8c6 |
| Last Changed Date: 2019-01-04 13:42:32 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:19 -0400 (Sat, 13 Apr 2019).
| Package 1101/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ORFik 1.2.1 Kornel Labun
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ORFik |
| Version: 1.2.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ORFik.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ORFik_1.2.1.tar.gz |
| StartedAt: 2019-04-13 04:19:37 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:26:51 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 433.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ORFik.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ORFik.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ORFik_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ORFik.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ORFik/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ORFik' version '1.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'ORFik' 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
assignTSSByCage: no visible global function definition for 'is'
computeFeatures: no visible global function definition for 'is'
computeFeatures: no visible binding for global variable 'entropyRFP'
computeFeatures: no visible binding for global variable
'disengagementScores'
computeFeatures: no visible binding for global variable 'RRS'
computeFeatures: no visible binding for global variable 'RSS'
computeFeatures: no visible binding for global variable
'fractionLengths'
computeFeatures: no visible binding for global variable 'te'
computeFeatures: no visible binding for global variable 'fpkmRFP'
computeFeatures: no visible binding for global variable 'fpkmRNA'
computeFeatures: no visible binding for global variable 'ORFScores'
computeFeatures: no visible binding for global variable 'ioScore'
computeFeatures: no visible binding for global variable 'inFrameCDS'
computeFeatures: no visible binding for global variable
'isOverlappingCds'
computeFeatures: no visible binding for global variable 'rankInTx'
computeFeaturesCage: no visible global function definition for 'is'
computeFeaturesCage: no visible binding for global variable
'entropyRFP'
computeFeaturesCage: no visible binding for global variable
'disengagementScores'
computeFeaturesCage: no visible binding for global variable 'RRS'
computeFeaturesCage: no visible binding for global variable 'RSS'
computeFeaturesCage: no visible binding for global variable
'fractionLengths'
computeFeaturesCage: no visible binding for global variable 'te'
computeFeaturesCage: no visible binding for global variable 'fpkmRFP'
computeFeaturesCage: no visible binding for global variable 'fpkmRNA'
computeFeaturesCage: no visible binding for global variable 'ORFScores'
computeFeaturesCage: no visible binding for global variable 'ioScore'
computeFeaturesCage: no visible binding for global variable
'inFrameCDS'
computeFeaturesCage: no visible binding for global variable
'isOverlappingCds'
computeFeaturesCage: no visible binding for global variable 'rankInTx'
convertToOneBasedRanges: no visible global function definition for '.'
disengagementScore: no visible global function definition for 'is'
extendLeaders: no visible global function definition for 'is'
findFa: no visible global function definition for 'is'
findORFsFasta: no visible global function definition for 'is'
groupGRangesBy: no visible global function definition for 'is'
insideOutsideORF: no visible global function definition for 'is'
kozakSequenceScore: no visible global function definition for 'is'
longestORFs: no visible global function definition for 'is'
longestORFs: no visible global function definition for '.'
mapToGRanges: no visible global function definition for 'is'
readWidths: no visible global function definition for 'is'
reassignTSSbyCage: no visible global function definition for 'is'
reassignTxDbByCage: no visible global function definition for 'is'
remakeTxdbExonIds: no visible global function definition for '.'
remakeTxdbExonIds: no visible binding for global variable 'chr'
removeTxdbExons: no visible binding for global variable 'exon_rank'
removeTxdbExons: no visible binding for global variable 'ranks'
ribosomeReleaseScore: no visible global function definition for 'is'
strandBool: no visible global function definition for 'is'
txNamesWithLeaders: no visible global function definition for 'is'
txSeqsFromFa: no visible global function definition for 'is'
Undefined global functions or variables:
. ORFScores RRS RSS chr disengagementScores entropyRFP exon_rank
fpkmRFP fpkmRNA fractionLengths inFrameCDS ioScore is
isOverlappingCds rankInTx ranks te
Consider adding
importFrom("methods", "is")
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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.8-bioc/R/library/ORFik/libs/i386/ORFik.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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
Examples with CPU or elapsed time > 5s
user system elapsed
computeFeatures 5.62 0.31 5.9
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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-3.8-bioc/meat/ORFik.Rcheck/00check.log'
for details.
ORFik.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ORFik_1.2.1.tar.gz && rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ORFik_1.2.1.zip && rm ORFik_1.2.1.tar.gz ORFik_1.2.1.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 295k 100 295k 0 0 7418k 0 --:--:-- --:--:-- --:--:-- 8202k
install for i386
* installing *source* package 'ORFik' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findOrfs.cpp -o findOrfs.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findOrfsFasta.cpp -o findOrfsFasta.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ORFik'
finding HTML links ... done
ORFik-package html
addCdsOnLeaderEnds html
addNewTSSOnLeaders html
asTX html
finding level-2 HTML links ... done
assignAnnotations html
assignFirstExonsStartSite html
assignLastExonsStopSite html
assignTSSByCage html
bedToGR html
changePointAnalysis html
checkRFP html
checkRNA html
codonSumsPerGroup html
computeFeatures html
computeFeaturesCage html
convertToOneBasedRanges html
coverageByWindow html
coveragePerTiling html
defineIsoform html
defineTrailer html
detectRibosomeShifts html
disengagementScore html
distToCds html
distToTSS html
downstreamFromPerGroup html
downstreamN html
downstreamOfPerGroup html
entropy html
extendLeaders html
extendsTSSexons html
filterCage html
findCageUTRFivelen html
findFa html
findMapORFs html
findMaxPeaks html
findNewTSS html
findORFs html
findORFsFasta html
firstEndPerGroup html
firstExonPerGroup html
firstStartPerGroup html
floss html
fpkm html
fpkm_calc html
fractionLength html
fread.bed html
gSort html
getStartStopWindows html
groupGRangesBy html
hasHits html
initiationScore html
insideOutsideORF html
is.gr_or_grl html
is.grl html
isInFrame html
isOverlapping html
isPeriodic html
kozakSequenceScore html
lastExonEndPerGroup html
lastExonPerGroup html
lastExonStartPerGroup html
longestORFs html
makeExonRanks html
makeORFNames html
mapToGRanges html
matchNaming html
metaWindow html
numExonsPerGroup html
orfID html
orfScore html
overlapsToCoverage html
parseCigar html
pmapFromTranscriptF html
rankOrder html
readWidths html
reassignTSSbyCage html
reassignTxDbByCage html
reduceKeepAttr html
regroupRleList html
remakeTxdbExonIds html
removeMetaCols html
removeTxdbExons html
restrictTSSByUpstreamLeader html
riboTISCoverageProportion html
ribosomeReleaseScore html
ribosomeStallingScore html
seqnamesPerGroup html
shiftFootprints html
sortPerGroup html
startCodons html
startDefinition html
startRegionString html
startSites html
stopCodons html
stopDefinition html
stopSites html
strandBool html
strandPerGroup html
subsetCoverage html
subset_to_frame html
tile1 html
translationalEff html
txLen html
txNames html
txNamesWithLeaders html
txSeqsFromFa html
uORFSearchSpace html
uniqueGroups html
uniqueOrder html
unlistGrl html
updateTxdbRanks html
updateTxdbStartSites html
upstreamFromPerGroup html
upstreamOfPerGroup html
validGRL html
widthPerGroup html
windowPerGroup html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ORFik' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findOrfs.cpp -o findOrfs.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c findOrfsFasta.cpp -o findOrfsFasta.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ORFik' as ORFik_1.2.1.zip
* DONE (ORFik)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ORFik' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
ORFik.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> library(testthat)
> library(ORFik)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
>
> test_check("ORFik")
== testthat results ===========================================================
OK: 236 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
31.09 1.53 32.67
|
ORFik.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> library(testthat)
> library(ORFik)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
>
> test_check("ORFik")
== testthat results ===========================================================
OK: 236 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
44.67 0.79 46.73
|
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ORFik.Rcheck/examples_i386/ORFik-Ex.timings
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ORFik.Rcheck/examples_x64/ORFik-Ex.timings
|