Nicholas Cooley
| Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: 5d0bdb6 |
| git_last_commit_date: 2025-02-03 12:50:44 -0500 (Mon, 03 Feb 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-04 11:43 -0500 (Tue, 04 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4716 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
| 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 2109/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.19.6 (landing page) Nicholas Cooley
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the SynExtend package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SynExtend.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 1.19.6 |
| 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_1.19.6.tar.gz |
| StartedAt: 2025-02-03 23:43:57 -0500 (Mon, 03 Feb 2025) |
| EndedAt: 2025-02-03 23:50:43 -0500 (Mon, 03 Feb 2025) |
| EllapsedTime: 405.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SynExtend.Rcheck |
| Warnings: 0 |
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### 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_1.19.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SynExtend.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.19.6’
* 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 14.0.0 (clang-1400.0.29.202)’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
installed size is 8.6Mb
sub-directories of 1Mb or more:
extdata 6.5Mb
* 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 code 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 ... NOTE
Unexported object imported by a ':::' call: ‘DECIPHER:::.detectCores’
See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
BlockExpansion.Rd: FindSynteny
BlockReconciliation.Rd: FindSynteny, Synteny-class
ClusterByK.Rd: FindSynteny
CompetePairs.Rd: FindSynteny
DisjointSet.Rd: FindSynteny, Synteny-class
EstimRearrScen.Rd: Synteny-class, FindSynteny
ExpandDiagonal.Rd: AlignPairs, FindSynteny
ExtractBy.Rd: FindSynteny, Synteny-class
NucleotideOverlap.Rd: FindSynteny, Synteny-class
PairSummaries.Rd: FindSynteny, Synteny-class
PrepareSeqs.Rd: FindSynteny
SelectByK.Rd: FindSynteny
SequenceSimilarity.Rd: AlignSeqs, AlignProfiles, AlignTranslation,
DistanceMatrix
SummarizePairs.Rd: SearchIndex, AlignProfiles, AlignPairs,
FindSynteny, IndexSeqs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 usage of KIND in Fortran files ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BuiltInEnsembles 94.732 2.960 98.220
ExampleStreptomycesData 65.855 1.730 67.996
BlockExpansion 38.918 0.829 40.018
ExpandDiagonal 18.758 0.665 19.551
SelectByK 13.354 0.330 13.782
SummarizePairs 12.886 0.362 13.351
predict.EvoWeaver 8.986 0.187 9.234
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/SynExtend.Rcheck/00check.log’
for details.
SynExtend.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SynExtend
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SynExtend’ ...
** this is package ‘SynExtend’ version ‘1.19.6’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CDend.c -o CDend.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CShuffle.c -o CShuffle.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HungarianAlgo.c -o HungarianAlgo.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LoserTree.c -o LoserTree.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MoranI.c -o MoranI.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NucleotideCounts.c -o NucleotideCounts.o
NucleotideCounts.c:267:7: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = INTEGER(NTHREADS)[0];
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OnDiskLP.c -o OnDiskLP.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PrefixTrie.c -o PrefixTrie.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_synextend.c -o R_init_synextend.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RandomForest.c -o RandomForest.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SEutils.c -o SEutils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XORRand.c -o XORRand.o
XORRand.c:67:7: warning: unused variable 'threads' [-Wunused-variable]
int threads = INTEGER(NTHREADS)[0];
^
1 warning generated.
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c _fortran_tabulate.f95 -o _fortran_tabulate.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c _fortran_utils.f95 -o _fortran_utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calcMIR2C.c -o calcMIR2C.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c cart_fort.f95 -o cart_fort.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dendrapply.c -o dendrapply.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o LoserTree.o MoranI.o NucleotideCounts.o OnDiskLP.o PrefixTrie.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o _fortran_tabulate.o _fortran_utils.o calcMIR2C.o cart_fort.o dendrapply.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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 | 38.918 | 0.829 | 40.018 | |
| BlockReconciliation | 0 | 0 | 0 | |
| BuiltInEnsembles | 94.732 | 2.960 | 98.220 | |
| CIDist_NullDist | 0.002 | 0.002 | 0.004 | |
| ClusterByK | 0.444 | 0.004 | 0.450 | |
| CompetePairs | 0.278 | 0.012 | 0.291 | |
| DPhyloStatistic | 0.036 | 0.002 | 0.038 | |
| DecisionTree-class | 0.042 | 0.002 | 0.044 | |
| DisjointSet | 0.054 | 0.003 | 0.057 | |
| Endosymbionts_GeneCalls | 0.021 | 0.002 | 0.023 | |
| Endosymbionts_LinkedFeatures | 0.021 | 0.002 | 0.023 | |
| Endosymbionts_Pairs01 | 0.030 | 0.002 | 0.031 | |
| Endosymbionts_Pairs02 | 0.031 | 0.003 | 0.034 | |
| Endosymbionts_Pairs03 | 0.027 | 0.002 | 0.029 | |
| Endosymbionts_Sets | 0.003 | 0.001 | 0.004 | |
| Endosymbionts_Synteny | 0.003 | 0.002 | 0.004 | |
| EstimRearrScen | 1.691 | 0.024 | 1.722 | |
| EstimateExoLabel | 0.003 | 0.001 | 0.003 | |
| EvoWeaver | 0.004 | 0.001 | 0.004 | |
| EvoWeb | 0.041 | 0.004 | 0.045 | |
| ExampleStreptomycesData | 65.855 | 1.730 | 67.996 | |
| ExoLabel | 0.061 | 0.046 | 0.115 | |
| ExpandDiagonal | 18.758 | 0.665 | 19.551 | |
| ExtractBy | 0.396 | 0.012 | 0.411 | |
| FastQFromSRR | 0 | 0 | 0 | |
| FindSets | 0.001 | 0.000 | 0.001 | |
| FitchParsimony | 0.076 | 0.002 | 0.080 | |
| Generic | 0.002 | 0.001 | 0.003 | |
| MakeBlastDb | 0 | 0 | 0 | |
| MoransI | 0.001 | 0.001 | 0.001 | |
| NucleotideOverlap | 0.460 | 0.006 | 0.470 | |
| PairSummaries | 4.582 | 0.062 | 4.667 | |
| PhyloDistance-CI | 0.004 | 0.002 | 0.006 | |
| PhyloDistance-JRF | 0.003 | 0.001 | 0.005 | |
| PhyloDistance-KF | 0.002 | 0.001 | 0.002 | |
| PhyloDistance-RF | 0.003 | 0.001 | 0.004 | |
| PhyloDistance | 0.003 | 0.000 | 0.004 | |
| PrepareSeqs | 0.023 | 0.002 | 0.026 | |
| RandForest | 0.016 | 0.001 | 0.016 | |
| SelectByK | 13.354 | 0.330 | 13.782 | |
| SequenceSimilarity | 0.066 | 0.002 | 0.069 | |
| SubSetPairs | 0.159 | 0.023 | 0.185 | |
| SummarizePairs | 12.886 | 0.362 | 13.351 | |
| SuperTree | 0.232 | 0.009 | 0.243 | |
| SuperTreeEx | 0.009 | 0.001 | 0.011 | |
| dendrapply | 0.117 | 0.015 | 0.133 | |
| gffToDataFrame | 4.439 | 0.029 | 4.493 | |
| plot.EvoWeb | 0.997 | 0.036 | 1.039 | |
| predict.EvoWeaver | 8.986 | 0.187 | 9.234 | |
| simMat | 0.021 | 0.003 | 0.025 | |
| subset-dendrogram | 0.390 | 0.010 | 0.404 | |