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This page was generated on 2024-04-18 11:32:20 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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 |
Package 2095/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SynExtend 1.14.0 (landing page) Nicholas Cooley
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | NA | ||||||||
To the developers/maintainers of the SynExtend package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SynExtend |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SynExtend_1.14.0.tar.gz |
StartedAt: 2024-04-18 05:52:52 -0400 (Thu, 18 Apr 2024) |
EndedAt: 2024-04-18 05:56:08 -0400 (Thu, 18 Apr 2024) |
EllapsedTime: 195.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SynExtend.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SynExtend_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SynExtend.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SynExtend/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SynExtend’ version ‘1.14.0’ * package encoding: UTF-8 * 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 ‘SynExtend’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 * 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 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 predict.EvoWeaver 14.586 1.210 16.512 BuiltInEnsembles 13.404 1.255 15.636 BlockExpansion 10.860 0.328 11.584 gffToDataFrame 5.763 0.048 5.949 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SynExtend.Rcheck/00check.log’ for details.
SynExtend.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SynExtend ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘SynExtend’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CDend.c -o CDend.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CShuffle.c -o CShuffle.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HungarianAlgo.c -o HungarianAlgo.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MoranI.c -o MoranI.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NucleotideCounts.c -o NucleotideCounts.o NucleotideCounts.c:252:7: warning: unused variable 'nthreads' [-Wunused-variable] int nthreads = INTEGER(NTHREADS)[0]; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_synextend.c -o R_init_synextend.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SEutils.c -o SEutils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XORRand.c -o XORRand.o XORRand.c:64:7: warning: unused variable 'threads' [-Wunused-variable] int threads = INTEGER(NTHREADS)[0]; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calcMIR2C.c -o calcMIR2C.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dendrapply.c -o dendrapply.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o MoranI.o NucleotideCounts.o R_init_synextend.o SEutils.o XORRand.o calcMIR2C.o dendrapply.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-SynExtend/00new/SynExtend/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 (SynExtend)
SynExtend.Rcheck/SynExtend-Ex.timings
name | user | system | elapsed | |
BlastSeqs | 0 | 0 | 0 | |
BlockExpansion | 10.860 | 0.328 | 11.584 | |
BlockReconciliation | 0.151 | 0.002 | 0.155 | |
BuiltInEnsembles | 13.404 | 1.255 | 15.636 | |
CIDist_NullDist | 0.001 | 0.002 | 0.004 | |
DPhyloStatistic | 0.046 | 0.002 | 0.050 | |
DisjointSet | 0.032 | 0.002 | 0.038 | |
Endosymbionts_GeneCalls | 0.017 | 0.003 | 0.020 | |
Endosymbionts_LinkedFeatures | 0.019 | 0.003 | 0.022 | |
Endosymbionts_Pairs01 | 0.017 | 0.003 | 0.021 | |
Endosymbionts_Pairs02 | 0.019 | 0.003 | 0.021 | |
Endosymbionts_Pairs03 | 0.018 | 0.003 | 0.022 | |
Endosymbionts_Sets | 0.002 | 0.003 | 0.005 | |
Endosymbionts_Synteny | 0.002 | 0.004 | 0.006 | |
EstimRearrScen | 1.341 | 0.028 | 1.378 | |
EvoWeaver | 0.003 | 0.001 | 0.004 | |
EvoWeb | 0.089 | 0.005 | 0.096 | |
ExampleStreptomycesData | 1.374 | 0.089 | 1.477 | |
ExtractBy | 0.289 | 0.013 | 0.306 | |
FastQFromSRR | 0 | 0 | 0 | |
FindSets | 0.001 | 0.000 | 0.002 | |
FitchParsimony | 0.084 | 0.005 | 0.090 | |
Generic | 0.003 | 0.003 | 0.006 | |
MakeBlastDb | 0 | 0 | 0 | |
MoransI | 0.001 | 0.000 | 0.002 | |
NucleotideOverlap | 0.269 | 0.004 | 0.277 | |
PairSummaries | 2.314 | 0.052 | 2.416 | |
PhyloDistance-CI | 0.005 | 0.001 | 0.007 | |
PhyloDistance-JRF | 0.003 | 0.001 | 0.003 | |
PhyloDistance-KF | 0.001 | 0.001 | 0.002 | |
PhyloDistance-RF | 0.002 | 0.000 | 0.003 | |
PhyloDistance | 0.003 | 0.000 | 0.004 | |
SelectByK | 0.153 | 0.006 | 0.164 | |
SequenceSimilarity | 0.089 | 0.006 | 0.096 | |
SubSetPairs | 0.053 | 0.007 | 0.062 | |
SuperTree | 1.160 | 0.030 | 1.232 | |
SuperTreeEx | 0.113 | 0.004 | 0.118 | |
dendrapply | 0.090 | 0.008 | 0.098 | |
gffToDataFrame | 5.763 | 0.048 | 5.949 | |
plot.EvoWeb | 0.627 | 0.014 | 0.663 | |
predict.EvoWeaver | 14.586 | 1.210 | 16.512 | |
simMat | 0.016 | 0.002 | 0.019 | |
subset-dendrogram | 0.057 | 0.005 | 0.065 | |