| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:53 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1994/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| syntenet 1.1.3 (landing page) FabrÃcio Almeida-Silva
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: syntenet |
| Version: 1.1.3 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:syntenet.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings syntenet_1.1.3.tar.gz |
| StartedAt: 2022-12-29 04:05:23 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 04:09:31 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 248.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: syntenet.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:syntenet.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings syntenet_1.1.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/syntenet.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'syntenet/DESCRIPTION' ... OK
* this is package 'syntenet' version '1.1.3'
* 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 whether package 'syntenet' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/syntenet/libs/x64/syntenet.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_profiles 5.14 0.04 5.19
* 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/syntenet.Rcheck/00check.log'
for details.
syntenet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL syntenet ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'syntenet' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mcscanxr.cpp -o mcscanxr.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/testthat/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o g++ -std=gnu++11 -shared -s -static-libgcc -o syntenet.dll tmp.def RcppExports.o mcscanxr.o test-runner.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-syntenet/00new/syntenet/libs/x64 ** 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 ** 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
29.95 3.56 33.93
syntenet.Rcheck/syntenet-Ex.timings
| name | user | system | elapsed | |
| angiosperm_phylogeny | 0 | 0 | 0 | |
| annotation | 0.01 | 0.00 | 0.02 | |
| binarize_and_transpose | 0.14 | 0.00 | 0.14 | |
| blast_list | 0.02 | 0.00 | 0.01 | |
| check_input | 0.14 | 0.05 | 0.19 | |
| cluster_network | 0.24 | 0.00 | 0.24 | |
| clusters | 0.02 | 0.01 | 0.03 | |
| diamond_is_installed | 0 | 0 | 0 | |
| edges | 0 | 0 | 0 | |
| fasta2AAStringSetlist | 0.04 | 0.00 | 0.05 | |
| find_GS_clusters | 4.24 | 0.21 | 4.44 | |
| gff2GRangesList | 0.12 | 0.01 | 0.14 | |
| infer_microsynteny_phylogeny | 0.11 | 0.02 | 0.12 | |
| infer_syntenet | 1.08 | 0.86 | 1.96 | |
| interspecies_synteny | 0.28 | 0.12 | 0.42 | |
| intraspecies_synteny | 0.33 | 0.27 | 0.61 | |
| iqtree_is_installed | 0.00 | 0.01 | 0.02 | |
| network | 0.18 | 0.00 | 0.19 | |
| parse_collinearity | 0 | 0 | 0 | |
| phylogenomic_profile | 0.11 | 0.02 | 0.12 | |
| plot_network | 1.10 | 0.02 | 1.11 | |
| plot_profiles | 5.14 | 0.04 | 5.19 | |
| process_input | 0.15 | 0.02 | 0.17 | |
| profiles2phylip | 0.22 | 0.00 | 0.22 | |
| proteomes | 0.08 | 0.00 | 0.08 | |
| run_diamond | 0.21 | 0.01 | 0.24 | |