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This page was generated on 2023-06-06 11:00:43 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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 2030/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.13.3 (landing page) Nicholas Cooley
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: SynExtend |
| Version: 1.13.3 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings SynExtend_1.13.3.tar.gz |
| StartedAt: 2023-06-06 08:18:15 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 08:22:03 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 228.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SynExtend.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings SynExtend_1.13.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SynExtend.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.13.3’
* 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 (GCC) 10.3.1’
* 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 18.888 0.428 19.334
BuiltInEnsembles 17.727 0.349 18.104
BlockExpansion 11.954 0.236 12.215
gffToDataFrame 9.538 0.175 9.755
* 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-3.18-bioc/meat/SynExtend.Rcheck/00check.log’
for details.
SynExtend.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL SynExtend ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘SynExtend’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c CDend.c -o CDend.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c CShuffle.c -o CShuffle.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c HungarianAlgo.c -o HungarianAlgo.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c MoranI.c -o MoranI.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c NucleotideCounts.c -o NucleotideCounts.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c R_init_synextend.c -o R_init_synextend.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c SEutils.c -o SEutils.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c XORRand.c -o XORRand.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c calcMIR2C.c -o calcMIR2C.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c dendrapply.c -o dendrapply.o gcc -shared -L/home/biocbuild/R/R-4.3.0/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/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 | 0 | 0 | |
| BlockExpansion | 11.954 | 0.236 | 12.215 | |
| BlockReconciliation | 0.216 | 0.000 | 0.216 | |
| BuiltInEnsembles | 17.727 | 0.349 | 18.104 | |
| CIDist_NullDist | 0.002 | 0.000 | 0.002 | |
| DPhyloStatistic | 0.042 | 0.003 | 0.045 | |
| DisjointSet | 0.028 | 0.000 | 0.029 | |
| Endosymbionts_GeneCalls | 0.009 | 0.004 | 0.013 | |
| Endosymbionts_LinkedFeatures | 0.013 | 0.000 | 0.014 | |
| Endosymbionts_Pairs01 | 0.013 | 0.000 | 0.014 | |
| Endosymbionts_Pairs02 | 0.013 | 0.000 | 0.014 | |
| Endosymbionts_Pairs03 | 0.013 | 0.000 | 0.014 | |
| Endosymbionts_Sets | 0.001 | 0.000 | 0.002 | |
| Endosymbionts_Synteny | 0.002 | 0.000 | 0.002 | |
| EstimRearrScen | 1.867 | 0.004 | 1.876 | |
| ExampleStreptomycesData | 2.089 | 0.130 | 2.224 | |
| ExtractBy | 0.268 | 0.016 | 0.285 | |
| FastQFromSRR | 0 | 0 | 0 | |
| FindSets | 0.001 | 0.000 | 0.002 | |
| Generic | 0.000 | 0.003 | 0.003 | |
| MakeBlastDb | 0 | 0 | 0 | |
| MoransI | 0.001 | 0.000 | 0.001 | |
| NucleotideOverlap | 0.343 | 0.008 | 0.351 | |
| PairSummaries | 2.647 | 0.056 | 2.708 | |
| PhyloDistance-CI | 0.005 | 0.000 | 0.005 | |
| PhyloDistance-JRF | 0.004 | 0.000 | 0.004 | |
| PhyloDistance-KF | 0.002 | 0.000 | 0.003 | |
| PhyloDistance-RF | 0.003 | 0.000 | 0.003 | |
| PhyloDistance | 0.005 | 0.000 | 0.005 | |
| ProtWeaver | 0.003 | 0.000 | 0.004 | |
| ProtWeb | 0.706 | 0.040 | 0.746 | |
| SelectByK | 0.148 | 0.000 | 0.148 | |
| SequenceSimilarity | 0.088 | 0.004 | 0.096 | |
| SubSetPairs | 0.062 | 0.008 | 0.070 | |
| SuperTree | 1.452 | 0.064 | 1.518 | |
| SuperTreeEx | 0.073 | 0.000 | 0.074 | |
| dendrapply | 0.158 | 0.003 | 0.161 | |
| gffToDataFrame | 9.538 | 0.175 | 9.755 | |
| plot.ProtWeb | 3.004 | 0.060 | 3.074 | |
| predict.ProtWeaver | 18.888 | 0.428 | 19.334 | |
| simMat | 0.023 | 0.000 | 0.023 | |