| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 2109/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| syntenet 1.8.1 (landing page) Fabrício Almeida-Silva
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the syntenet package: - 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 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: syntenet |
| Version: 1.8.1 |
| 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_1.8.1.tar.gz |
| StartedAt: 2024-12-20 10:33:54 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 10:43:09 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 554.5 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_1.8.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/syntenet.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘syntenet/DESCRIPTION’ ... OK
* this is package ‘syntenet’ version ‘1.8.1’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 13.564 0.362 14.182
plot_profiles 5.782 0.214 6.164
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘syntenet’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mcscanxr.cpp -o mcscanxr.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.4-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 Olucimarinus.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 Olucimarinus.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 OspRCC809.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 Olucimarinus.collinearity
Tandem pairs written to Olucimarinus.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 OspRCC809.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 102 ]
>
> proc.time()
user system elapsed
58.684 2.477 62.276
syntenet.Rcheck/syntenet-Ex.timings
| name | user | system | elapsed | |
| angiosperm_phylogeny | 0.004 | 0.003 | 0.007 | |
| annotation | 0.016 | 0.003 | 0.019 | |
| binarize_and_transpose | 0.264 | 0.022 | 0.287 | |
| blast_list | 0.030 | 0.004 | 0.034 | |
| check_input | 0.401 | 0.040 | 0.443 | |
| cluster_network | 0.606 | 0.020 | 0.636 | |
| clusters | 0.061 | 0.002 | 0.065 | |
| collapse_protein_ids | 0.766 | 0.010 | 0.785 | |
| create_species_id_table | 0.144 | 0.005 | 0.149 | |
| diamond_is_installed | 0.004 | 0.009 | 0.016 | |
| edges | 0.005 | 0.002 | 0.006 | |
| export_sequences | 0.580 | 0.072 | 0.658 | |
| fasta2AAStringSetlist | 0.023 | 0.005 | 0.029 | |
| find_GS_clusters | 13.564 | 0.362 | 14.182 | |
| gff2GRangesList | 0.363 | 0.005 | 0.378 | |
| infer_microsynteny_phylogeny | 0.270 | 0.021 | 0.298 | |
| infer_syntenet | 0.930 | 0.035 | 0.971 | |
| interspecies_synteny | 0.626 | 0.018 | 0.647 | |
| intraspecies_synteny | 0.477 | 0.028 | 0.538 | |
| iqtree_is_installed | 0.009 | 0.014 | 0.031 | |
| iqtree_version | 0.007 | 0.015 | 0.027 | |
| last_is_installed | 0.003 | 0.009 | 0.013 | |
| network | 0.479 | 0.005 | 0.486 | |
| parse_collinearity | 0.007 | 0.002 | 0.008 | |
| phylogenomic_profile | 0.248 | 0.004 | 0.253 | |
| plot_network | 3.486 | 0.048 | 3.577 | |
| plot_profiles | 5.782 | 0.214 | 6.164 | |
| process_input | 0.437 | 0.007 | 0.460 | |
| profiles2phylip | 0.372 | 0.008 | 0.400 | |
| proteomes | 0.141 | 0.005 | 0.148 | |
| read_diamond | 0.004 | 0.001 | 0.006 | |
| run_diamond | 0.436 | 0.016 | 0.457 | |
| run_last | 0.447 | 0.015 | 0.465 | |
| scerevisiae_annot | 0.016 | 0.002 | 0.019 | |
| scerevisiae_diamond | 0.055 | 0.003 | 0.058 | |