| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:29 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the DECIPHER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DECIPHER.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 496/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 2.29.0 (landing page) Erik Wright
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | |||||||||
| Package: DECIPHER |
| Version: 2.29.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DECIPHER_2.29.0.tar.gz |
| StartedAt: 2023-06-05 20:50:51 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 21:30:52 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: DECIPHER.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DECIPHER_2.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DECIPHER.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.29.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 13.3Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 7.5Mb
extdata 2.3Mb
libs 1.8Mb
* 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
* 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 ... NOTE
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’
TreeLine: multiple local function definitions for ‘.minimize’ with
different formal arguments
Undefined global functions or variables:
deltaGrulesRNA deltaHrules deltaHrulesRNA
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MapCharacters 109.332 0.220 109.773
FindNonCoding 100.025 0.615 100.836
LearnNonCoding 75.676 1.239 77.023
ExtractGenes 51.759 0.228 52.061
WriteGenes 49.997 0.088 50.181
Genes-class 49.793 0.088 49.957
FindGenes 47.955 0.052 48.090
BrowseSeqs 28.699 0.212 28.962
AlignSeqs 27.097 0.395 27.541
DetectRepeats 22.749 0.096 22.878
CorrectFrameshifts 20.559 0.099 20.694
StaggerAlignment 17.755 0.095 17.884
LearnTaxa 16.171 0.207 16.405
AlignTranslation 14.603 0.100 14.732
Taxa-class 13.079 0.044 13.150
IdTaxa 11.627 0.043 11.688
TreeLine 10.815 0.044 10.883
Clusterize 9.129 0.068 9.213
ScoreAlignment 6.944 0.044 7.001
TileSeqs 5.996 0.008 6.018
Array2Matrix 5.342 0.052 5.403
DesignArray 5.221 0.008 5.237
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘ArtOfAlignmentInR.Rnw’... OK
‘ClassifySequences.Rnw’... OK
‘ClusteringSequences.Rnw’... OK
‘DECIPHERing.Rnw’... OK
‘DesignMicroarray.Rnw’... OK
‘DesignPrimers.Rnw’... OK
‘DesignProbes.Rnw’... OK
‘DesignSignatures.Rnw’... OK
‘FindChimeras.Rnw’... OK
‘FindingGenes.Rnw’... OK
‘FindingNonCodingRNAs.Rnw’... OK
‘GrowingTrees.Rnw’... OK
‘RepeatRepeat.Rnw’... OK
OK
* checking re-building of vignette outputs ...
DECIPHER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL DECIPHER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘DECIPHER’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c AlignProfiles.c -o AlignProfiles.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c AssignIndels.c -o AssignIndels.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c CalculateDeltaG.c -o CalculateDeltaG.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c CalculateFISH.c -o CalculateFISH.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c ChainSegments.c -o ChainSegments.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Cluster.c -o Cluster.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c ClusterML.c -o ClusterML.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c ClusterMP.c -o ClusterMP.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c CommonGaps.c -o CommonGaps.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Compositions.c -o Compositions.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Compression.c -o Compression.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c ConsensusSequence.c -o ConsensusSequence.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c ConsolidateGaps.c -o ConsolidateGaps.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c DesignProbes.c -o DesignProbes.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Diff.c -o Diff.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c DistanceMatrix.c -o DistanceMatrix.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c EnumerateSequence.c -o EnumerateSequence.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c FindFrameshifts.c -o FindFrameshifts.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c GeneFinding.c -o GeneFinding.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c GetPools.c -o GetPools.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Import.c -o Import.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c InformationContent.c -o InformationContent.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c InsertGaps.c -o InsertGaps.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c IntDist.c -o IntDist.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c MeltPolymer.c -o MeltPolymer.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c MovingAverage.c -o MovingAverage.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c MultiMatch.c -o MultiMatch.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c NNLS.c -o NNLS.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Order.c -o Order.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c PairwiseAlignment.c -o PairwiseAlignment.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c PredictDBN.c -o PredictDBN.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c PredictHEC.c -o PredictHEC.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c R_init_decipher.c -o R_init_decipher.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c RawVectors.c -o RawVectors.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c RemoveGaps.c -o RemoveGaps.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c ReplaceChars.c -o ReplaceChars.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c SphericalKmeans.c -o SphericalKmeans.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c TerminalMismatch.c -o TerminalMismatch.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c Translate.c -o Translate.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c VectorSums.c -o VectorSums.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o ClusterMP.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o RawVectors.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o SphericalKmeans.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DECIPHER)
DECIPHER.Rcheck/DECIPHER-Ex.timings
| name | user | system | elapsed | |
| AA_REDUCED | 0.053 | 0.008 | 0.061 | |
| Add2DB | 0.313 | 0.008 | 0.324 | |
| AdjustAlignment | 0.251 | 0.010 | 0.263 | |
| AlignDB | 1.484 | 0.062 | 1.551 | |
| AlignProfiles | 0.822 | 0.016 | 0.845 | |
| AlignSeqs | 27.097 | 0.395 | 27.541 | |
| AlignSynteny | 3.648 | 0.040 | 3.694 | |
| AlignTranslation | 14.603 | 0.100 | 14.732 | |
| AmplifyDNA | 0.003 | 0.000 | 0.004 | |
| Array2Matrix | 5.342 | 0.052 | 5.403 | |
| BrowseDB | 0.373 | 0.000 | 0.373 | |
| BrowseSeqs | 28.699 | 0.212 | 28.962 | |
| CalculateEfficiencyArray | 0.016 | 0.000 | 0.016 | |
| CalculateEfficiencyFISH | 0.006 | 0.000 | 0.006 | |
| CalculateEfficiencyPCR | 0.005 | 0.000 | 0.006 | |
| Clusterize | 9.129 | 0.068 | 9.213 | |
| Codec | 1.359 | 0.012 | 1.373 | |
| ConsensusSequence | 0.219 | 0.012 | 0.231 | |
| Cophenetic | 0.225 | 0.000 | 0.226 | |
| CorrectFrameshifts | 20.559 | 0.099 | 20.694 | |
| CreateChimeras | 0.994 | 0.004 | 1.000 | |
| DB2Seqs | 0.02 | 0.00 | 0.02 | |
| DesignArray | 5.221 | 0.008 | 5.237 | |
| DesignPrimers | 0.001 | 0.000 | 0.001 | |
| DesignProbes | 0.001 | 0.000 | 0.001 | |
| DesignSignatures | 0.001 | 0.000 | 0.001 | |
| DetectRepeats | 22.749 | 0.096 | 22.878 | |
| DigestDNA | 0.199 | 0.000 | 0.198 | |
| Disambiguate | 0.063 | 0.004 | 0.067 | |
| DistanceMatrix | 0.058 | 0.000 | 0.058 | |
| ExtractGenes | 51.759 | 0.228 | 52.061 | |
| FindChimeras | 0.091 | 0.000 | 0.091 | |
| FindGenes | 47.955 | 0.052 | 48.090 | |
| FindNonCoding | 100.025 | 0.615 | 100.836 | |
| FindSynteny | 1.758 | 0.016 | 1.777 | |
| FormGroups | 0.059 | 0.004 | 0.063 | |
| Genes-class | 49.793 | 0.088 | 49.957 | |
| HEC_MI | 0.211 | 0.000 | 0.212 | |
| IdConsensus | 0.888 | 0.012 | 0.902 | |
| IdLengths | 0.022 | 0.000 | 0.022 | |
| IdTaxa | 11.627 | 0.043 | 11.688 | |
| IdentifyByRank | 0.027 | 0.004 | 0.032 | |
| LearnNonCoding | 75.676 | 1.239 | 77.023 | |
| LearnTaxa | 16.171 | 0.207 | 16.405 | |
| MIQS | 0.036 | 0.008 | 0.044 | |
| MODELS | 0.002 | 0.000 | 0.002 | |
| MapCharacters | 109.332 | 0.220 | 109.773 | |
| MaskAlignment | 0.643 | 0.008 | 0.652 | |
| MeltDNA | 0.053 | 0.000 | 0.053 | |
| NNLS | 0.004 | 0.000 | 0.004 | |
| NonCoding-class | 0.049 | 0.008 | 0.057 | |
| NonCodingRNA | 0.097 | 0.004 | 0.100 | |
| OrientNucleotides | 1.137 | 0.000 | 1.138 | |
| PFASUM | 0.024 | 0.000 | 0.024 | |
| PredictDBN | 0.011 | 0.004 | 0.015 | |
| PredictHEC | 0.252 | 0.000 | 0.253 | |
| RESTRICTION_ENZYMES | 0.000 | 0.003 | 0.003 | |
| ReadDendrogram | 0.016 | 0.001 | 0.016 | |
| RemoveGaps | 0.015 | 0.000 | 0.015 | |
| ScoreAlignment | 6.944 | 0.044 | 7.001 | |
| SearchDB | 0.038 | 0.004 | 0.043 | |
| Seqs2DB | 0.105 | 0.004 | 0.110 | |
| StaggerAlignment | 17.755 | 0.095 | 17.884 | |
| Synteny-class | 2.966 | 0.008 | 2.980 | |
| Taxa-class | 13.079 | 0.044 | 13.150 | |
| TerminalChar | 0.016 | 0.000 | 0.017 | |
| TileSeqs | 5.996 | 0.008 | 6.018 | |
| TrainingSet_16S | 3.007 | 0.048 | 3.062 | |
| TreeLine | 10.815 | 0.044 | 10.883 | |
| TrimDNA | 0.180 | 0.004 | 0.185 | |
| WriteDendrogram | 0.005 | 0.000 | 0.005 | |
| WriteGenes | 49.997 | 0.088 | 50.181 | |
| deltaGrules | 0.011 | 0.000 | 0.011 | |
| deltaGrulesRNA | 0.021 | 0.000 | 0.021 | |
| deltaHrules | 0.018 | 0.000 | 0.019 | |
| deltaHrulesRNA | 0.017 | 0.000 | 0.017 | |
| deltaSrules | 0.052 | 0.000 | 0.053 | |
| deltaSrulesRNA | 0.016 | 0.000 | 0.016 | |