| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:32 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1997/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.11.6 (landing page) Nicholas Cooley
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: SynExtend |
| Version: 1.11.6 |
| 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/library --timings SynExtend_1.11.6.tar.gz |
| StartedAt: 2023-02-07 17:17:05 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 17:21:22 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 256.5 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/library --timings SynExtend_1.11.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SynExtend.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.11.6’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 19.850 0.080 23.125
BuiltInEnsembles 17.640 0.042 19.137
BlockExpansion 12.134 0.165 12.906
gffToDataFrame 9.373 0.003 10.159
* 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
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SynExtend ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘SynExtend’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ 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 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 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 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o SynExtend.so CDend.o CShuffle.o MoranI.o NucleotideCounts.o R_init_synextend.o SEutils.o XORRand.o calcMIR2C.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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 | 12.134 | 0.165 | 12.906 | |
| BlockReconciliation | 0.2 | 0.0 | 0.2 | |
| BuiltInEnsembles | 17.640 | 0.042 | 19.137 | |
| DPhyloStatistic | 0.043 | 0.000 | 0.042 | |
| DisjointSet | 0.027 | 0.000 | 0.030 | |
| Endosymbionts_GeneCalls | 0.013 | 0.000 | 0.030 | |
| Endosymbionts_LinkedFeatures | 0.012 | 0.003 | 0.030 | |
| Endosymbionts_Pairs01 | 0.014 | 0.000 | 0.031 | |
| Endosymbionts_Pairs02 | 0.014 | 0.000 | 0.030 | |
| Endosymbionts_Pairs03 | 0.015 | 0.000 | 0.028 | |
| Endosymbionts_Sets | 0.002 | 0.000 | 0.002 | |
| Endosymbionts_Synteny | 0.002 | 0.000 | 0.003 | |
| EstimRearrScen | 1.782 | 0.000 | 1.888 | |
| ExampleStreptomycesData | 1.846 | 0.008 | 2.002 | |
| ExtractBy | 0.257 | 0.000 | 0.256 | |
| FindSets | 0.002 | 0.000 | 0.002 | |
| Generic | 0.003 | 0.000 | 0.003 | |
| MoransI | 0.001 | 0.000 | 0.002 | |
| NucleotideOverlap | 0.377 | 0.000 | 0.394 | |
| PairSummaries | 2.746 | 0.024 | 3.057 | |
| PhyloDistance-GRF | 0.004 | 0.000 | 0.004 | |
| PhyloDistance-JRF | 0.004 | 0.000 | 0.011 | |
| PhyloDistance-KF | 0.002 | 0.000 | 0.003 | |
| PhyloDistance-RF | 0.003 | 0.000 | 0.019 | |
| PhyloDistance | 0.005 | 0.000 | 0.005 | |
| ProtWeaver | 0.003 | 0.000 | 0.003 | |
| ProtWeb | 0.690 | 0.004 | 0.853 | |
| SelectByK | 0.134 | 0.000 | 0.187 | |
| SequenceSimilarity | 0.077 | 0.008 | 0.172 | |
| SubSetPairs | 0.063 | 0.000 | 0.127 | |
| SuperTree | 3.672 | 0.087 | 3.925 | |
| SuperTreeEx | 0.089 | 0.000 | 0.089 | |
| gffToDataFrame | 9.373 | 0.003 | 10.159 | |
| plot.ProtWeb | 2.675 | 0.004 | 2.949 | |
| predict.ProtWeaver | 19.850 | 0.080 | 23.125 | |
| simMat | 0.014 | 0.000 | 0.014 | |