Nicholas Cooley
| Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: b53bf4f |
| git_last_commit_date: 2024-02-28 16:10:12 -0500 (Wed, 28 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:40:03 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 2077/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.15.2 (landing page) Nicholas Cooley
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.15.2 |
| 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_1.15.2.tar.gz |
| StartedAt: 2024-03-02 11:33:40 -0500 (Sat, 02 Mar 2024) |
| EndedAt: 2024-03-02 11:40:29 -0500 (Sat, 02 Mar 2024) |
| EllapsedTime: 408.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SynExtend.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.15.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SynExtend.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.15.2’
* 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 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 34.321 1.095 40.733
BuiltInEnsembles 31.795 0.999 37.418
BlockExpansion 20.342 0.474 24.064
gffToDataFrame 16.468 0.159 19.699
PairSummaries 4.040 0.079 5.173
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/library’
* installing *source* package ‘SynExtend’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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 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:252:7: 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 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 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:64:7: warning: unused variable 'threads' [-Wunused-variable]
int threads = 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 calcMIR2C.c -o calcMIR2C.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 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/4.4-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 | 0.000 | 0.001 | 0.001 | |
| BlockExpansion | 20.342 | 0.474 | 24.064 | |
| BlockReconciliation | 0.403 | 0.005 | 0.463 | |
| BuiltInEnsembles | 31.795 | 0.999 | 37.418 | |
| CIDist_NullDist | 0.002 | 0.003 | 0.008 | |
| DPhyloStatistic | 0.074 | 0.004 | 0.104 | |
| DisjointSet | 0.049 | 0.007 | 0.080 | |
| Endosymbionts_GeneCalls | 0.022 | 0.004 | 0.033 | |
| Endosymbionts_LinkedFeatures | 0.023 | 0.003 | 0.034 | |
| Endosymbionts_Pairs01 | 0.022 | 0.004 | 0.032 | |
| Endosymbionts_Pairs02 | 0.024 | 0.004 | 0.032 | |
| Endosymbionts_Pairs03 | 0.022 | 0.003 | 0.032 | |
| Endosymbionts_Sets | 0.003 | 0.003 | 0.007 | |
| Endosymbionts_Synteny | 0.003 | 0.003 | 0.008 | |
| EstimRearrScen | 3.259 | 0.051 | 4.030 | |
| EvoWeaver | 0.006 | 0.003 | 0.010 | |
| EvoWeb | 0.189 | 0.013 | 0.250 | |
| ExampleStreptomycesData | 2.559 | 0.094 | 3.374 | |
| ExtractBy | 0.442 | 0.013 | 0.567 | |
| FastQFromSRR | 0.000 | 0.001 | 0.001 | |
| FindSets | 0.002 | 0.001 | 0.003 | |
| FitchParsimony | 0.195 | 0.006 | 0.254 | |
| Generic | 0.004 | 0.004 | 0.008 | |
| MakeBlastDb | 0.000 | 0.001 | 0.001 | |
| MoransI | 0.002 | 0.000 | 0.003 | |
| NucleotideOverlap | 0.609 | 0.010 | 0.766 | |
| PairSummaries | 4.040 | 0.079 | 5.173 | |
| PhyloDistance-CI | 0.008 | 0.002 | 0.012 | |
| PhyloDistance-JRF | 0.007 | 0.001 | 0.010 | |
| PhyloDistance-KF | 0.004 | 0.000 | 0.008 | |
| PhyloDistance-RF | 0.005 | 0.001 | 0.009 | |
| PhyloDistance | 0.009 | 0.001 | 0.012 | |
| PrepareSeqs | 3.565 | 0.043 | 4.558 | |
| SelectByK | 0.177 | 0.005 | 0.226 | |
| SequenceSimilarity | 0.136 | 0.010 | 0.187 | |
| SubSetPairs | 0.081 | 0.005 | 0.113 | |
| SuperTree | 2.237 | 0.033 | 2.830 | |
| SuperTreeEx | 0.107 | 0.002 | 0.141 | |
| dendrapply | 0.244 | 0.037 | 0.398 | |
| gffToDataFrame | 16.468 | 0.159 | 19.699 | |
| plot.EvoWeb | 1.638 | 0.036 | 1.927 | |
| predict.EvoWeaver | 34.321 | 1.095 | 40.733 | |
| simMat | 0.042 | 0.011 | 0.062 | |
| subset-dendrogram | 0.130 | 0.008 | 0.156 | |