Nicholas Cooley
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: RELEASE_3_19 |
| git_last_commit: 4426e94 |
| git_last_commit_date: 2024-04-30 11:23:46 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:47 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 2121/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.16.0 (landing page) Nicholas Cooley
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
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: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2024-05-07 01:22:42 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 01:24:54 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 131.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SynExtend.Rcheck |
| Warnings: 1 |
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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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/SynExtend.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.16.0’
* 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-1500.1.0.2.5)’
* 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 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 ... WARNING
'library' or 'require' call not declared from: ‘RSQLite’
'library' or 'require' call to ‘RSQLite’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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 ... NOTE
prepare_Rd: EstimateExoLabel.Rd:41-43: Dropping empty section \references
checkRd: (-1) ExampleStreptomycesData.Rd:8: Lost braces; missing escapes or markup?
8 | Data from {Streptomyces} species to test \code{\link{EvoWeaver}} functionality.
| ^
* 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
ExpandDiagonal 24.327 0.512 24.858
BlockExpansion 20.914 0.222 21.141
SelectByK 13.482 0.289 13.789
SummarizePairs 12.241 0.130 12.372
predict.EvoWeaver 4.619 0.446 5.102
* 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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/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-arm64/Resources/library’
* installing *source* package ‘SynExtend’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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 OnDiskLP.c -o OnDiskLP.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 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 OnDiskLP.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-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 | 20.914 | 0.222 | 21.141 | |
| BlockReconciliation | 0.001 | 0.000 | 0.000 | |
| BuiltInEnsembles | 4.088 | 0.324 | 4.440 | |
| CIDist_NullDist | 0.000 | 0.001 | 0.002 | |
| ClusterByK | 1.511 | 0.013 | 1.524 | |
| DPhyloStatistic | 0.012 | 0.000 | 0.012 | |
| DisjointSet | 0.028 | 0.001 | 0.030 | |
| Endosymbionts_GeneCalls | 0.003 | 0.001 | 0.005 | |
| Endosymbionts_LinkedFeatures | 0.011 | 0.001 | 0.013 | |
| Endosymbionts_Pairs01 | 0.011 | 0.001 | 0.011 | |
| Endosymbionts_Pairs02 | 0.011 | 0.001 | 0.011 | |
| Endosymbionts_Pairs03 | 0.009 | 0.001 | 0.010 | |
| Endosymbionts_Sets | 0.002 | 0.001 | 0.002 | |
| Endosymbionts_Synteny | 0.006 | 0.002 | 0.008 | |
| EstimRearrScen | 0.469 | 0.010 | 0.480 | |
| EstimateExoLabel | 0.001 | 0.000 | 0.000 | |
| EvoWeaver | 0.001 | 0.000 | 0.001 | |
| EvoWeb | 0.023 | 0.001 | 0.025 | |
| ExampleStreptomycesData | 0.418 | 0.032 | 0.453 | |
| ExoLabel | 0.004 | 0.005 | 0.009 | |
| ExpandDiagonal | 24.327 | 0.512 | 24.858 | |
| ExtractBy | 0.120 | 0.004 | 0.122 | |
| FastQFromSRR | 0 | 0 | 0 | |
| FindSets | 0 | 0 | 0 | |
| FitchParsimony | 0.020 | 0.001 | 0.021 | |
| Generic | 0.000 | 0.001 | 0.001 | |
| MakeBlastDb | 0 | 0 | 0 | |
| MoransI | 0 | 0 | 0 | |
| NucleotideOverlap | 0.346 | 0.005 | 0.351 | |
| PairSummaries | 1.190 | 0.074 | 1.264 | |
| PhyloDistance-CI | 0.001 | 0.000 | 0.002 | |
| PhyloDistance-JRF | 0.000 | 0.001 | 0.001 | |
| PhyloDistance-KF | 0 | 0 | 0 | |
| PhyloDistance-RF | 0.001 | 0.000 | 0.001 | |
| PhyloDistance | 0.001 | 0.000 | 0.001 | |
| PrepareSeqs | 0.591 | 0.011 | 0.606 | |
| SelectByK | 13.482 | 0.289 | 13.789 | |
| SequenceSimilarity | 0.027 | 0.001 | 0.029 | |
| SubSetPairs | 0.199 | 0.059 | 0.261 | |
| SummarizePairs | 12.241 | 0.130 | 12.372 | |
| SuperTree | 0.212 | 0.005 | 0.216 | |
| SuperTreeEx | 0.028 | 0.000 | 0.028 | |
| dendrapply | 0.025 | 0.003 | 0.028 | |
| gffToDataFrame | 1.724 | 0.013 | 1.739 | |
| plot.EvoWeb | 0.197 | 0.008 | 0.207 | |
| predict.EvoWeaver | 4.619 | 0.446 | 5.102 | |
| simMat | 0.003 | 0.000 | 0.004 | |
| subset-dendrogram | 0.011 | 0.001 | 0.013 | |