| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:42 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2037/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.11.7 (landing page) Nicholas Cooley
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: SynExtend |
| Version: 1.11.7 |
| 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_1.11.7.tar.gz |
| StartedAt: 2023-04-12 09:49:41 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 09:52:48 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 186.6 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_1.11.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SynExtend.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.11.7’
* 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* 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 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 11.730 0.113 11.841
BuiltInEnsembles 11.544 0.169 11.713
BlockExpansion 9.851 0.277 10.129
gffToDataFrame 5.699 0.000 5.700
* 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 | 0.000 | 0.000 | 0.001 | |
| BlockExpansion | 9.851 | 0.277 | 10.129 | |
| BlockReconciliation | 0.131 | 0.001 | 0.131 | |
| BuiltInEnsembles | 11.544 | 0.169 | 11.713 | |
| CIDist_NullDist | 0.001 | 0.000 | 0.001 | |
| DPhyloStatistic | 0.030 | 0.003 | 0.034 | |
| DisjointSet | 0.023 | 0.000 | 0.022 | |
| Endosymbionts_GeneCalls | 0.012 | 0.000 | 0.012 | |
| Endosymbionts_LinkedFeatures | 0.013 | 0.000 | 0.013 | |
| Endosymbionts_Pairs01 | 0.013 | 0.000 | 0.013 | |
| Endosymbionts_Pairs02 | 0.012 | 0.000 | 0.013 | |
| Endosymbionts_Pairs03 | 0.013 | 0.000 | 0.012 | |
| Endosymbionts_Sets | 0.002 | 0.000 | 0.001 | |
| Endosymbionts_Synteny | 0.002 | 0.000 | 0.002 | |
| EstimRearrScen | 1.209 | 0.004 | 1.214 | |
| ExampleStreptomycesData | 1.247 | 0.092 | 1.339 | |
| ExtractBy | 0.214 | 0.012 | 0.227 | |
| FindSets | 0.001 | 0.000 | 0.001 | |
| Generic | 0.002 | 0.000 | 0.002 | |
| MoransI | 0.001 | 0.000 | 0.001 | |
| NucleotideOverlap | 0.255 | 0.004 | 0.259 | |
| PairSummaries | 1.542 | 0.008 | 1.550 | |
| PhyloDistance-CI | 0.004 | 0.000 | 0.004 | |
| PhyloDistance-JRF | 0.004 | 0.000 | 0.003 | |
| 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 | 0.419 | 0.004 | 0.423 | |
| SelectByK | 0.097 | 0.000 | 0.097 | |
| SequenceSimilarity | 0.067 | 0.000 | 0.068 | |
| SubSetPairs | 0.042 | 0.004 | 0.046 | |
| SuperTree | 2.332 | 0.116 | 2.448 | |
| SuperTreeEx | 0.073 | 0.000 | 0.073 | |
| dendrapply | 0.104 | 0.004 | 0.108 | |
| gffToDataFrame | 5.699 | 0.000 | 5.700 | |
| plot.ProtWeb | 1.546 | 0.000 | 1.546 | |
| predict.ProtWeaver | 11.730 | 0.113 | 11.841 | |
| simMat | 0.004 | 0.004 | 0.009 | |