| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:33 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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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 496/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 2.29.0 (landing page) Erik Wright
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / 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: 2023-05-30 05:09:40 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 05:49:40 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 2400.1 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 (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* 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 (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking installed package size ... NOTE
installed size is 12.9Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 7.5Mb
extdata 2.3Mb
libs 1.3Mb
* 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 106.211 0.404 106.613
FindNonCoding 99.879 0.632 100.508
LearnNonCoding 74.318 3.496 77.814
WriteGenes 50.294 0.184 50.478
ExtractGenes 49.294 0.396 49.689
Genes-class 47.617 0.172 47.787
FindGenes 46.532 0.140 46.670
BrowseSeqs 28.878 0.264 29.169
AlignSeqs 26.945 0.604 27.550
DetectRepeats 22.634 0.136 22.770
CorrectFrameshifts 18.912 0.124 19.035
StaggerAlignment 17.533 0.200 17.734
LearnTaxa 15.645 0.528 16.172
AlignTranslation 14.399 0.132 14.537
Taxa-class 13.221 0.052 13.274
IdTaxa 11.907 0.052 11.959
TreeLine 11.126 0.076 11.202
Clusterize 8.945 0.108 9.053
ScoreAlignment 6.804 0.036 6.840
TileSeqs 5.757 0.012 5.768
Array2Matrix 5.493 0.068 5.560
DesignArray 5.411 0.044 5.455
* 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 (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ 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 | 0.062 | 0.000 | 0.061 | |
| Add2DB | 0.329 | 0.008 | 0.341 | |
| AdjustAlignment | 0.255 | 0.000 | 0.258 | |
| AlignDB | 1.575 | 0.088 | 1.667 | |
| AlignProfiles | 0.842 | 0.032 | 0.879 | |
| AlignSeqs | 26.945 | 0.604 | 27.550 | |
| AlignSynteny | 3.394 | 0.056 | 3.451 | |
| AlignTranslation | 14.399 | 0.132 | 14.537 | |
| AmplifyDNA | 0.004 | 0.000 | 0.005 | |
| Array2Matrix | 5.493 | 0.068 | 5.560 | |
| BrowseDB | 0.03 | 0.00 | 0.03 | |
| BrowseSeqs | 28.878 | 0.264 | 29.169 | |
| CalculateEfficiencyArray | 0.019 | 0.000 | 0.019 | |
| CalculateEfficiencyFISH | 0.006 | 0.000 | 0.006 | |
| CalculateEfficiencyPCR | 0.005 | 0.000 | 0.005 | |
| Clusterize | 8.945 | 0.108 | 9.053 | |
| Codec | 1.324 | 0.000 | 1.325 | |
| ConsensusSequence | 0.210 | 0.008 | 0.219 | |
| Cophenetic | 0.21 | 0.00 | 0.21 | |
| CorrectFrameshifts | 18.912 | 0.124 | 19.035 | |
| CreateChimeras | 0.942 | 0.000 | 0.942 | |
| DB2Seqs | 0.016 | 0.004 | 0.021 | |
| DesignArray | 5.411 | 0.044 | 5.455 | |
| DesignPrimers | 0.001 | 0.000 | 0.001 | |
| DesignProbes | 0.001 | 0.000 | 0.001 | |
| DesignSignatures | 0.001 | 0.000 | 0.002 | |
| DetectRepeats | 22.634 | 0.136 | 22.770 | |
| DigestDNA | 0.184 | 0.008 | 0.192 | |
| Disambiguate | 0.068 | 0.000 | 0.068 | |
| DistanceMatrix | 0.062 | 0.008 | 0.070 | |
| ExtractGenes | 49.294 | 0.396 | 49.689 | |
| FindChimeras | 0.082 | 0.000 | 0.082 | |
| FindGenes | 46.532 | 0.140 | 46.670 | |
| FindNonCoding | 99.879 | 0.632 | 100.508 | |
| FindSynteny | 1.781 | 0.028 | 1.809 | |
| FormGroups | 0.060 | 0.004 | 0.063 | |
| Genes-class | 47.617 | 0.172 | 47.787 | |
| HEC_MI | 0.232 | 0.004 | 0.237 | |
| IdConsensus | 0.878 | 0.012 | 0.889 | |
| IdLengths | 0.023 | 0.000 | 0.023 | |
| IdTaxa | 11.907 | 0.052 | 11.959 | |
| IdentifyByRank | 0.028 | 0.004 | 0.032 | |
| LearnNonCoding | 74.318 | 3.496 | 77.814 | |
| LearnTaxa | 15.645 | 0.528 | 16.172 | |
| MIQS | 0.051 | 0.000 | 0.050 | |
| MODELS | 0.002 | 0.000 | 0.002 | |
| MapCharacters | 106.211 | 0.404 | 106.613 | |
| MaskAlignment | 0.607 | 0.016 | 0.623 | |
| MeltDNA | 0.049 | 0.004 | 0.053 | |
| NNLS | 0.004 | 0.000 | 0.004 | |
| NonCoding-class | 0.059 | 0.000 | 0.059 | |
| NonCodingRNA | 0.103 | 0.000 | 0.104 | |
| OrientNucleotides | 0.987 | 0.004 | 0.991 | |
| PFASUM | 0.031 | 0.000 | 0.032 | |
| PredictDBN | 0.015 | 0.000 | 0.014 | |
| PredictHEC | 0.268 | 0.004 | 0.272 | |
| RESTRICTION_ENZYMES | 0.004 | 0.000 | 0.003 | |
| ReadDendrogram | 0.017 | 0.000 | 0.017 | |
| RemoveGaps | 0.015 | 0.000 | 0.015 | |
| ScoreAlignment | 6.804 | 0.036 | 6.840 | |
| SearchDB | 0.041 | 0.000 | 0.042 | |
| Seqs2DB | 0.103 | 0.004 | 0.106 | |
| StaggerAlignment | 17.533 | 0.200 | 17.734 | |
| Synteny-class | 2.770 | 0.000 | 2.772 | |
| Taxa-class | 13.221 | 0.052 | 13.274 | |
| TerminalChar | 0.012 | 0.004 | 0.016 | |
| TileSeqs | 5.757 | 0.012 | 5.768 | |
| TrainingSet_16S | 3.002 | 0.012 | 3.015 | |
| TreeLine | 11.126 | 0.076 | 11.202 | |
| TrimDNA | 0.159 | 0.004 | 0.162 | |
| WriteDendrogram | 0.004 | 0.000 | 0.005 | |
| WriteGenes | 50.294 | 0.184 | 50.478 | |
| deltaGrules | 0.012 | 0.000 | 0.012 | |
| deltaGrulesRNA | 0.018 | 0.004 | 0.022 | |
| deltaHrules | 0.019 | 0.000 | 0.019 | |
| deltaHrulesRNA | 0.019 | 0.000 | 0.019 | |
| deltaSrules | 0.059 | 0.004 | 0.063 | |
| deltaSrulesRNA | 0.017 | 0.000 | 0.017 | |