Wenjun Liu
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/sSNAPPY |
| git_branch: RELEASE_3_16 |
| git_last_commit: 483e456 |
| git_last_commit_date: 2023-03-28 20:18:03 -0400 (Tue, 28 Mar 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:28 -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 sSNAPPY package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sSNAPPY.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 1965/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sSNAPPY 1.2.5 (landing page) Wenjun Liu
| 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: sSNAPPY |
| Version: 1.2.5 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sSNAPPY_1.2.5.tar.gz |
| StartedAt: 2023-04-10 22:56:16 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:02:27 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 371.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sSNAPPY.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sSNAPPY_1.2.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/sSNAPPY.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 ‘sSNAPPY/DESCRIPTION’ ... OK
* this is package ‘sSNAPPY’ version ‘1.2.5’
* 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 ‘sSNAPPY’ 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 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
rank_gene_pert 46.473 1.891 48.466
pathway_pert 35.006 1.770 36.864
plot_gene_contribution 28.829 1.795 30.713
raw_gene_pert 28.240 1.656 29.986
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
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/sSNAPPY.Rcheck/00check.log’
for details.
sSNAPPY.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sSNAPPY
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘sSNAPPY’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c GenePertScore.cpp -o GenePertScore.o
In file included from GenePertScore.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo:26:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:338:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
#pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:343:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
#pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:346:11: warning: INFO: see the documentation for details [-W#pragma-messages]
#pragma message ("INFO: see the documentation for details")
^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c code.cpp -o code.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c normaliseByPermutation.cpp -o normaliseByPermutation.o
In file included from normaliseByPermutation.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo:26:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:338:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
#pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:343:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
#pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:346:11: warning: INFO: see the documentation for details [-W#pragma-messages]
#pragma message ("INFO: see the documentation for details")
^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 sSNAPPY.so GenePertScore.o RcppExports.o code.o normaliseByPermutation.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-sSNAPPY/00new/sSNAPPY/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 (sSNAPPY)
sSNAPPY.Rcheck/tests/spelling.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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.186 0.065 0.243
sSNAPPY.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(sSNAPPY)
>
> test_check("sSNAPPY")
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
warning: solve(): system is singular; attempting approx solution
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 115 ]
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 115 ]
>
> proc.time()
user system elapsed
38.163 6.016 33.163
sSNAPPY.Rcheck/sSNAPPY-Ex.timings
| name | user | system | elapsed | |
| generate_permuted_scores | 0.273 | 0.008 | 0.281 | |
| normalise_by_permu | 0.001 | 0.001 | 0.001 | |
| pathway_pert | 35.006 | 1.770 | 36.864 | |
| plot_community | 2.032 | 0.056 | 2.100 | |
| plot_gene_contribution | 28.829 | 1.795 | 30.713 | |
| plot_gs2gene | 3.200 | 0.054 | 3.260 | |
| plot_gs_network | 0.531 | 0.007 | 0.539 | |
| rank_gene_pert | 46.473 | 1.891 | 48.466 | |
| raw_gene_pert | 28.240 | 1.656 | 29.986 | |
| retrieve_topology | 0.807 | 0.006 | 0.814 | |
| weight_ss_fc | 0.279 | 0.005 | 0.285 | |