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 11:05:20 -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: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings sSNAPPY_1.2.5.tar.gz |
| StartedAt: 2023-04-11 00:19:49 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:28:11 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 502.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sSNAPPY.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings sSNAPPY_1.2.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/sSNAPPY.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
libs 4.0Mb
* 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 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 ... 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 55.465 0.824 56.291
pathway_pert 41.840 1.704 43.546
plot_gene_contribution 34.631 0.927 35.559
raw_gene_pert 33.999 0.592 34.592
* 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 ...
‘sSNAPPY.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/sSNAPPY.Rcheck/00check.log’
for details.
sSNAPPY.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL sSNAPPY
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘sSNAPPY’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GenePertScore.cpp -o GenePertScore.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/armadillo:26,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from GenePertScore.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:338:86: note: #pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:343:75: note: #pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:346:61: note: #pragma message: INFO: see the documentation for details
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c code.cpp -o code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c normaliseByPermutation.cpp -o normaliseByPermutation.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/armadillo:26,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from normaliseByPermutation.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:338:86: note: #pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed
338 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:343:75: note: #pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead
343 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:346:61: note: #pragma message: INFO: see the documentation for details
346 | #pragma message ("INFO: see the documentation for details")
| ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o sSNAPPY.so GenePertScore.o RcppExports.o code.o normaliseByPermutation.o -fopenmp -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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-pc-linux-gnu (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
0.154 0.034 0.173
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-pc-linux-gnu (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
38.073 4.165 33.536
sSNAPPY.Rcheck/sSNAPPY-Ex.timings
| name | user | system | elapsed | |
| generate_permuted_scores | 0.314 | 0.008 | 0.322 | |
| normalise_by_permu | 0 | 0 | 0 | |
| pathway_pert | 41.840 | 1.704 | 43.546 | |
| plot_community | 2.205 | 0.025 | 2.229 | |
| plot_gene_contribution | 34.631 | 0.927 | 35.559 | |
| plot_gs2gene | 4.476 | 0.040 | 4.517 | |
| plot_gs_network | 0.694 | 0.000 | 0.694 | |
| rank_gene_pert | 55.465 | 0.824 | 56.291 | |
| raw_gene_pert | 33.999 | 0.592 | 34.592 | |
| retrieve_topology | 0.887 | 0.008 | 0.896 | |
| weight_ss_fc | 0.276 | 0.020 | 0.296 | |