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 11:35:49 -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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SynExtend_1.12.0.tar.gz |
| StartedAt: 2023-10-16 01:37:58 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 01:40:54 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 175.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SynExtend.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SynExtend_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SynExtend.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SynExtend’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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.ProtWeaver 11.254 0.504 11.807
BuiltInEnsembles 10.826 0.216 11.075
BlockExpansion 9.006 0.255 9.263
gffToDataFrame 5.730 0.032 5.763
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘UsingSynExtend.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SynExtend.Rcheck/00check.log’
for details.
SynExtend.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SynExtend
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘SynExtend’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CDend.c -o CDend.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CShuffle.c -o CShuffle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c HungarianAlgo.c -o HungarianAlgo.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MoranI.c -o MoranI.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c NucleotideCounts.c -o NucleotideCounts.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_synextend.c -o R_init_synextend.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SEutils.c -o SEutils.o
SEutils.c: In function ‘genCostMatrix’:
SEutils.c:197:26: warning: ‘row’ may be used uninitialized in this function [-Wmaybe-uninitialized]
197 | idxLookup[j*nc1+i] = row;
| ~~~~~~~~~~~~~~~~~~~^~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XORRand.c -o XORRand.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c calcMIR2C.c -o calcMIR2C.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c dendrapply.c -o dendrapply.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/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 -fopenmp -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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 | 0.001 | 0.001 | 0.000 | |
| BlockExpansion | 9.006 | 0.255 | 9.263 | |
| BlockReconciliation | 0.144 | 0.000 | 0.144 | |
| BuiltInEnsembles | 10.826 | 0.216 | 11.075 | |
| CIDist_NullDist | 0.001 | 0.000 | 0.001 | |
| DPhyloStatistic | 0.030 | 0.004 | 0.034 | |
| DisjointSet | 0.021 | 0.004 | 0.025 | |
| Endosymbionts_GeneCalls | 0.012 | 0.000 | 0.012 | |
| Endosymbionts_LinkedFeatures | 0.005 | 0.008 | 0.013 | |
| Endosymbionts_Pairs01 | 0.013 | 0.000 | 0.012 | |
| Endosymbionts_Pairs02 | 0.013 | 0.000 | 0.013 | |
| Endosymbionts_Pairs03 | 0.009 | 0.004 | 0.012 | |
| Endosymbionts_Sets | 0.002 | 0.000 | 0.001 | |
| Endosymbionts_Synteny | 0.000 | 0.002 | 0.002 | |
| EstimRearrScen | 1.213 | 0.037 | 1.251 | |
| ExampleStreptomycesData | 0.970 | 0.024 | 1.015 | |
| ExtractBy | 0.206 | 0.000 | 0.206 | |
| FindSets | 0.001 | 0.000 | 0.001 | |
| Generic | 0.002 | 0.000 | 0.002 | |
| MoransI | 0.001 | 0.000 | 0.001 | |
| NucleotideOverlap | 0.247 | 0.000 | 0.247 | |
| PairSummaries | 1.792 | 0.064 | 1.855 | |
| PhyloDistance-CI | 0.005 | 0.000 | 0.005 | |
| PhyloDistance-JRF | 0.004 | 0.000 | 0.004 | |
| PhyloDistance-KF | 0.002 | 0.000 | 0.002 | |
| PhyloDistance-RF | 0.002 | 0.000 | 0.002 | |
| PhyloDistance | 0.003 | 0.000 | 0.003 | |
| ProtWeaver | 0.003 | 0.000 | 0.003 | |
| ProtWeb | 0.430 | 0.004 | 0.450 | |
| SelectByK | 0.088 | 0.000 | 0.087 | |
| SequenceSimilarity | 0.067 | 0.000 | 0.068 | |
| SubSetPairs | 0.043 | 0.000 | 0.044 | |
| SuperTree | 1.959 | 0.080 | 2.040 | |
| SuperTreeEx | 0.070 | 0.004 | 0.075 | |
| dendrapply | 0.104 | 0.008 | 0.113 | |
| gffToDataFrame | 5.730 | 0.032 | 5.763 | |
| plot.ProtWeb | 1.762 | 0.016 | 1.778 | |
| predict.ProtWeaver | 11.254 | 0.504 | 11.807 | |
| simMat | 0.011 | 0.000 | 0.010 | |