Nicholas Cooley
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: RELEASE_3_17 |
| git_last_commit: 5d59cf3 |
| git_last_commit_date: 2023-04-25 11:18:00 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:43 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 2059/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.12.0 (landing page) Nicholas Cooley
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.12.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SynExtend.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SynExtend_1.12.0.tar.gz |
| StartedAt: 2023-10-16 07:30:23 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 07:33:22 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 178.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SynExtend.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SynExtend.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SynExtend_1.12.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/SynExtend.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SynExtend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SynExtend' version '1.12.0'
* 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 whether package 'SynExtend' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/SynExtend/libs/x64/SynExtend.dll':
Found '_assert', possibly from 'assert' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BlockExpansion 10.42 1.27 12.19
predict.ProtWeaver 11.20 0.48 15.95
BuiltInEnsembles 10.58 0.62 15.24
gffToDataFrame 5.59 0.10 5.72
* 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
'F:/biocbuild/bbs-3.17-bioc/meat/SynExtend.Rcheck/00check.log'
for details.
SynExtend.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SynExtend
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'SynExtend' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CDend.c -o CDend.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CShuffle.c -o CShuffle.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HungarianAlgo.c -o HungarianAlgo.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MoranI.c -o MoranI.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NucleotideCounts.c -o NucleotideCounts.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_synextend.c -o R_init_synextend.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SEutils.c -o SEutils.o
SEutils.c: In function 'genCostMatrix':
SEutils.c:197:26: warning: 'row' may be used uninitialized [-Wmaybe-uninitialized]
197 | idxLookup[j*nc1+i] = row;
| ~~~~~~~~~~~~~~~~~~~^~~~~
SEutils.c:182:19: note: 'row' was declared here
182 | int col1, col2, row;
| ^~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XORRand.c -o XORRand.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcMIR2C.c -o calcMIR2C.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dendrapply.c -o dendrapply.o
gcc -shared -s -static-libgcc -o SynExtend.dll tmp.def CDend.o CShuffle.o HungarianAlgo.o MoranI.o NucleotideCounts.o R_init_synextend.o SEutils.o XORRand.o calcMIR2C.o dendrapply.o -fopenmp -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-SynExtend/00new/SynExtend/libs/x64
** 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
** 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 | 10.42 | 1.27 | 12.19 | |
| BlockReconciliation | 0.11 | 0.00 | 0.11 | |
| BuiltInEnsembles | 10.58 | 0.62 | 15.24 | |
| CIDist_NullDist | 0 | 0 | 0 | |
| DPhyloStatistic | 0.03 | 0.02 | 0.04 | |
| DisjointSet | 0.00 | 0.03 | 0.03 | |
| Endosymbionts_GeneCalls | 0.02 | 0.00 | 0.02 | |
| Endosymbionts_LinkedFeatures | 0.00 | 0.01 | 0.02 | |
| Endosymbionts_Pairs01 | 0.00 | 0.02 | 0.01 | |
| Endosymbionts_Pairs02 | 0.00 | 0.01 | 0.02 | |
| Endosymbionts_Pairs03 | 0.01 | 0.00 | 0.02 | |
| Endosymbionts_Sets | 0.00 | 0.02 | 0.01 | |
| Endosymbionts_Synteny | 0.02 | 0.00 | 0.02 | |
| EstimRearrScen | 1.55 | 0.00 | 1.59 | |
| ExampleStreptomycesData | 1.25 | 0.03 | 1.28 | |
| ExtractBy | 0.17 | 0.01 | 0.19 | |
| FindSets | 0 | 0 | 0 | |
| Generic | 0.01 | 0.00 | 0.02 | |
| MoransI | 0 | 0 | 0 | |
| NucleotideOverlap | 0.21 | 0.03 | 0.23 | |
| PairSummaries | 1.65 | 0.02 | 1.67 | |
| PhyloDistance-CI | 0.02 | 0.00 | 0.02 | |
| PhyloDistance-JRF | 0 | 0 | 0 | |
| PhyloDistance-KF | 0 | 0 | 0 | |
| PhyloDistance-RF | 0.01 | 0.00 | 0.01 | |
| PhyloDistance | 0 | 0 | 0 | |
| ProtWeaver | 0 | 0 | 0 | |
| ProtWeb | 0.74 | 0.00 | 0.74 | |
| SelectByK | 0.11 | 0.00 | 0.11 | |
| SequenceSimilarity | 0.06 | 0.02 | 0.20 | |
| SubSetPairs | 0.03 | 0.00 | 0.03 | |
| SuperTree | 2.58 | 0.25 | 2.83 | |
| SuperTreeEx | 0.06 | 0.00 | 0.06 | |
| dendrapply | 0.1 | 0.0 | 0.1 | |
| gffToDataFrame | 5.59 | 0.10 | 5.72 | |
| plot.ProtWeb | 1.30 | 0.02 | 1.31 | |
| predict.ProtWeaver | 11.20 | 0.48 | 15.95 | |
| simMat | 0.01 | 0.00 | 0.02 | |