| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:29 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 syntenet package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/syntenet.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 2013/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| syntenet 1.0.4 (landing page) Fabrício Almeida-Silva
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: syntenet |
| Version: 1.0.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:syntenet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings syntenet_1.0.4.tar.gz |
| StartedAt: 2023-04-10 23:01:54 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:05:48 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 234.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: syntenet.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:syntenet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings syntenet_1.0.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/syntenet.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘syntenet/DESCRIPTION’ ... OK
* this is package ‘syntenet’ version ‘1.0.4’
* 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 ‘syntenet’ can be installed ... OK
* 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
find_GS_clusters 4.882 0.142 5.036
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/syntenet.Rcheck/00check.log’
for details.
syntenet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL syntenet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘syntenet’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mcscanxr.cpp -o mcscanxr.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o syntenet.so RcppExports.o mcscanxr.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-syntenet/00new/syntenet/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (syntenet)
syntenet.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(syntenet)
>
> test_check("syntenet")
Reading GFF file and pre-processing
Reading BLAST file and pre-processing
Generating BLAST list
match_list.size: 172
172 matches imported (171 discarded)
6 pairwise comparisons
0 alignments generated
Pairwise collinear blocks written to Olu.collinearity
Done!
Reading GFF file and pre-processing
Reading BLAST file and pre-processing
Generating BLAST list
match_list.size: 19
19 matches imported (17 discarded)
6 pairwise comparisons
0 alignments generated
Pairwise collinear blocks written to Osp.collinearity
Done!
Reading GFF file and pre-processing
Reading BLAST file and pre-processing
Generating BLAST list
match_list.size: 1267
1267 matches imported (1257 discarded)
9 pairwise comparisons
8 alignments generated
Pairwise collinear blocks written to Olucimarinus_OspRCC809.collinearity
Done!
Reading GFF file and pre-processing
Reading BLAST file and pre-processing
Generating BLAST list
match_list.size: 172
172 matches imported (171 discarded)
6 pairwise comparisons
0 alignments generated
Pairwise collinear blocks written to Olu.collinearity
Tandem pairs written to Olu.tandem
Writing multiple syntenic blocks to HTML files
Olu_Chr_1.html
Olu_Chr_2.html
Olu_Chr_3.html
Done!
Reading GFF file and pre-processing
Reading BLAST file and pre-processing
Generating BLAST list
match_list.size: 19
19 matches imported (17 discarded)
6 pairwise comparisons
0 alignments generated
Pairwise collinear blocks written to Osp.collinearity
Writing multiple syntenic blocks to HTML files
Osp_chr_1.html
Osp_chr_2.html
Osp_chr_3.html
Done!
Reading GFF file and pre-processing
Reading BLAST file and pre-processing
Generating BLAST list
match_list.size: 1267
1267 matches imported (1257 discarded)
9 pairwise comparisons
8 alignments generated
Pairwise collinear blocks written to Olucimarinus_OspRCC809.collinearity
Writing multiple syntenic blocks to HTML files
Olu_Chr_1.html
Olu_Chr_2.html
Olu_Chr_3.html
Osp_chr_1.html
Osp_chr_2.html
Osp_chr_3.html
Done!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 78 ]
>
> proc.time()
user system elapsed
23.275 0.921 24.273
syntenet.Rcheck/syntenet-Ex.timings
| name | user | system | elapsed | |
| angiosperm_phylogeny | 0.003 | 0.002 | 0.005 | |
| annotation | 0.009 | 0.001 | 0.010 | |
| binarize_and_transpose | 0.132 | 0.004 | 0.137 | |
| blast_list | 0.014 | 0.001 | 0.015 | |
| check_input | 0.158 | 0.004 | 0.162 | |
| cluster_network | 0.293 | 0.006 | 0.301 | |
| clusters | 0.031 | 0.001 | 0.032 | |
| diamond_is_installed | 0.004 | 0.005 | 0.015 | |
| edges | 0.002 | 0.001 | 0.003 | |
| fasta2AAStringSetlist | 0.040 | 0.003 | 0.044 | |
| find_GS_clusters | 4.882 | 0.142 | 5.036 | |
| gff2GRangesList | 0.184 | 0.003 | 0.189 | |
| infer_microsynteny_phylogeny | 0.138 | 0.008 | 0.154 | |
| infer_syntenet | 0.400 | 0.016 | 0.418 | |
| interspecies_synteny | 0.130 | 0.006 | 0.138 | |
| intraspecies_synteny | 0.062 | 0.005 | 0.067 | |
| iqtree_is_installed | 0.003 | 0.006 | 0.013 | |
| network | 0.277 | 0.003 | 0.280 | |
| parse_collinearity | 0.003 | 0.001 | 0.003 | |
| phylogenomic_profile | 0.120 | 0.002 | 0.122 | |
| plot_network | 1.344 | 0.028 | 1.375 | |
| plot_profiles | 3.259 | 0.086 | 3.349 | |
| process_input | 0.178 | 0.002 | 0.182 | |
| profiles2phylip | 0.157 | 0.010 | 0.176 | |
| proteomes | 0.081 | 0.003 | 0.083 | |
| run_diamond | 0.197 | 0.008 | 0.212 | |