Nicholas Cooley
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: b53bf4f |
| git_last_commit_date: 2024-02-28 16:10:12 -0400 (Wed, 28 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:11 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 2093/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.15.2 (landing page) Nicholas Cooley
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.15.2 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SynExtend_1.15.2.tar.gz |
| StartedAt: 2024-03-28 03:15:04 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:18:03 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 178.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SynExtend.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SynExtend_1.15.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SynExtend.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.15.2’
* 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 code 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 ... NOTE
checkRd: (-1) ExampleStreptomycesData.Rd:8: Lost braces; missing escapes or markup?
8 | Data from {Streptomyces} species to test \code{\link{EvoWeaver}} functionality.
| ^
* 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.EvoWeaver 12.118 0.202 12.377
BuiltInEnsembles 11.017 0.174 11.231
BlockExpansion 9.698 0.299 10.001
gffToDataFrame 5.861 0.072 5.934
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/SynExtend.Rcheck/00check.log’
for details.
SynExtend.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SynExtend ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CDend.c -o CDend.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CShuffle.c -o CShuffle.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c HungarianAlgo.c -o HungarianAlgo.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MoranI.c -o MoranI.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c NucleotideCounts.c -o NucleotideCounts.o gcc -I"/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SEutils.c -o SEutils.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XORRand.c -o XORRand.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c calcMIR2C.c -o calcMIR2C.o gcc -I"/home/biocbuild/bbs-3.19-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-3.19-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-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-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 | 0.000 | 0.000 | |
| BlockExpansion | 9.698 | 0.299 | 10.001 | |
| BlockReconciliation | 0.131 | 0.004 | 0.136 | |
| BuiltInEnsembles | 11.017 | 0.174 | 11.231 | |
| CIDist_NullDist | 0.002 | 0.000 | 0.001 | |
| DPhyloStatistic | 0.032 | 0.004 | 0.036 | |
| DisjointSet | 0.021 | 0.004 | 0.025 | |
| Endosymbionts_GeneCalls | 0.013 | 0.000 | 0.013 | |
| Endosymbionts_LinkedFeatures | 0.014 | 0.000 | 0.014 | |
| Endosymbionts_Pairs01 | 0.010 | 0.004 | 0.014 | |
| Endosymbionts_Pairs02 | 0.010 | 0.004 | 0.014 | |
| Endosymbionts_Pairs03 | 0.014 | 0.000 | 0.014 | |
| Endosymbionts_Sets | 0.000 | 0.001 | 0.002 | |
| Endosymbionts_Synteny | 0.001 | 0.002 | 0.002 | |
| EstimRearrScen | 1.497 | 0.036 | 1.533 | |
| EvoWeaver | 0.004 | 0.000 | 0.003 | |
| EvoWeb | 0.08 | 0.00 | 0.08 | |
| ExampleStreptomycesData | 1.284 | 0.088 | 1.394 | |
| ExtractBy | 0.238 | 0.008 | 0.246 | |
| FastQFromSRR | 0.000 | 0.001 | 0.001 | |
| FindSets | 0.000 | 0.002 | 0.002 | |
| FitchParsimony | 0.070 | 0.025 | 0.094 | |
| Generic | 0.002 | 0.000 | 0.003 | |
| MakeBlastDb | 0 | 0 | 0 | |
| MoransI | 0.001 | 0.000 | 0.001 | |
| NucleotideOverlap | 0.232 | 0.007 | 0.240 | |
| PairSummaries | 1.569 | 0.040 | 1.609 | |
| PhyloDistance-CI | 0.004 | 0.000 | 0.005 | |
| PhyloDistance-JRF | 0.004 | 0.000 | 0.004 | |
| PhyloDistance-KF | 0.270 | 0.036 | 0.306 | |
| PhyloDistance-RF | 0.002 | 0.000 | 0.002 | |
| PhyloDistance | 0.004 | 0.000 | 0.003 | |
| PrepareSeqs | 1.355 | 0.036 | 1.391 | |
| SelectByK | 0.096 | 0.000 | 0.096 | |
| SequenceSimilarity | 0.068 | 0.012 | 0.080 | |
| SubSetPairs | 0.051 | 0.004 | 0.054 | |
| SuperTree | 0.656 | 0.020 | 0.676 | |
| SuperTreeEx | 0.073 | 0.000 | 0.072 | |
| dendrapply | 0.087 | 0.012 | 0.099 | |
| gffToDataFrame | 5.861 | 0.072 | 5.934 | |
| plot.EvoWeb | 0.506 | 0.027 | 0.535 | |
| predict.EvoWeaver | 12.118 | 0.202 | 12.377 | |
| simMat | 0.017 | 0.000 | 0.017 | |
| subset-dendrogram | 0.041 | 0.008 | 0.049 | |