Nicholas Cooley
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: 7cdfb94 |
| git_last_commit_date: 2024-04-30 11:23:46 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:21 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 2056/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.17.0 (landing page) Nicholas Cooley
| kjohnson1 | macOS 13.6.6 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: 1.17.0 |
| 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_1.17.0.tar.gz |
| StartedAt: 2024-05-20 04:42:28 -0400 (Mon, 20 May 2024) |
| EndedAt: 2024-05-20 04:49:53 -0400 (Mon, 20 May 2024) |
| EllapsedTime: 444.4 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_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/SynExtend.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.17.0’
* 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 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 85.783 2.095 88.255
BlockExpansion 79.050 1.378 81.062
SelectByK 48.468 1.066 49.757
SummarizePairs 45.656 0.973 46.977
predict.EvoWeaver 13.930 1.008 15.113
BuiltInEnsembles 12.932 0.948 14.030
gffToDataFrame 5.639 0.038 5.700
* 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-3.20-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-1500.0.40.1)’
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 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 | 79.050 | 1.378 | 81.062 | |
| BlockReconciliation | 0.000 | 0.001 | 0.000 | |
| BuiltInEnsembles | 12.932 | 0.948 | 14.030 | |
| CIDist_NullDist | 0.002 | 0.002 | 0.004 | |
| ClusterByK | 4.834 | 0.045 | 4.888 | |
| DPhyloStatistic | 0.046 | 0.002 | 0.047 | |
| DisjointSet | 0.097 | 0.004 | 0.101 | |
| Endosymbionts_GeneCalls | 0.015 | 0.002 | 0.017 | |
| Endosymbionts_LinkedFeatures | 0.038 | 0.002 | 0.041 | |
| Endosymbionts_Pairs01 | 0.033 | 0.002 | 0.035 | |
| Endosymbionts_Pairs02 | 0.033 | 0.002 | 0.035 | |
| Endosymbionts_Pairs03 | 0.031 | 0.003 | 0.034 | |
| Endosymbionts_Sets | 0.004 | 0.002 | 0.006 | |
| Endosymbionts_Synteny | 0.019 | 0.002 | 0.022 | |
| EstimRearrScen | 1.683 | 0.021 | 1.708 | |
| EstimateExoLabel | 0.000 | 0.001 | 0.001 | |
| EvoWeaver | 0.002 | 0.001 | 0.003 | |
| EvoWeb | 0.086 | 0.005 | 0.091 | |
| ExampleStreptomycesData | 1.377 | 0.095 | 1.484 | |
| ExoLabel | 0.013 | 0.014 | 0.031 | |
| ExpandDiagonal | 85.783 | 2.095 | 88.255 | |
| ExtractBy | 0.375 | 0.010 | 0.385 | |
| FastQFromSRR | 0 | 0 | 0 | |
| FindSets | 0.002 | 0.000 | 0.002 | |
| FitchParsimony | 0.071 | 0.003 | 0.074 | |
| Generic | 0.003 | 0.002 | 0.005 | |
| MakeBlastDb | 0 | 0 | 0 | |
| MoransI | 0.002 | 0.000 | 0.002 | |
| NucleotideOverlap | 1.192 | 0.021 | 1.215 | |
| PairSummaries | 3.742 | 0.138 | 3.891 | |
| PhyloDistance-CI | 0.005 | 0.001 | 0.006 | |
| PhyloDistance-JRF | 0.003 | 0.001 | 0.004 | |
| PhyloDistance-KF | 0.001 | 0.001 | 0.001 | |
| PhyloDistance-RF | 0.001 | 0.000 | 0.002 | |
| PhyloDistance | 0.002 | 0.000 | 0.003 | |
| PrepareSeqs | 1.904 | 0.034 | 1.949 | |
| SelectByK | 48.468 | 1.066 | 49.757 | |
| SequenceSimilarity | 0.088 | 0.004 | 0.092 | |
| SubSetPairs | 0.576 | 0.079 | 0.661 | |
| SummarizePairs | 45.656 | 0.973 | 46.977 | |
| SuperTree | 0.736 | 0.021 | 0.759 | |
| SuperTreeEx | 0.094 | 0.003 | 0.099 | |
| dendrapply | 0.101 | 0.013 | 0.114 | |
| gffToDataFrame | 5.639 | 0.038 | 5.700 | |
| plot.EvoWeb | 0.644 | 0.016 | 0.662 | |
| predict.EvoWeaver | 13.930 | 1.008 | 15.113 | |
| simMat | 0.014 | 0.001 | 0.015 | |
| subset-dendrogram | 0.041 | 0.006 | 0.049 | |