Damian Szklarczyk
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/STRINGdb |
| Branch: RELEASE_3_10 |
| Last Commit: 848db67 |
| Last Changed Date: 2019-10-29 13:08:48 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:22:11 -0400 (Wed, 15 Apr 2020).
| Package 1678/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| STRINGdb 1.26.0 Damian Szklarczyk
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: STRINGdb |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STRINGdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings STRINGdb_1.26.0.tar.gz |
| StartedAt: 2020-04-15 06:57:28 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:05:35 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 487.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: STRINGdb.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STRINGdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings STRINGdb_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/STRINGdb.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'STRINGdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'STRINGdb' version '1.26.0'
* 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 'STRINGdb' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
coeffOfvar: no visible global function definition for 'sd'
downloadAbsentFile: no visible global function definition for 'tail'
downloadAbsentFile: no visible global function definition for
'download.file'
downloadAbsentFileSTRING: no visible global function definition for
'read.table'
downloadAbsentFileSTRING: no visible global function definition for
'tail'
downloadAbsentFileSTRING: no visible global function definition for
'download.file'
get_STRING_species: no visible global function definition for
'read.table'
plot_ppi_enrichment_graph: no visible global function definition for
'pdf'
plot_ppi_enrichment_graph: no visible global function definition for
'jpeg'
plot_ppi_enrichment_graph: no visible global function definition for
'plot'
plot_ppi_enrichment_graph: no visible global function definition for
'abline'
plot_ppi_enrichment_graph: no visible global function definition for
'dev.off'
ppi_enrichment: no visible global function definition for 'ppois'
ppi_enrichment_full: no visible global function definition for
'txtProgressBar'
ppi_enrichment_full: no visible global function definition for
'setTxtProgressBar'
ppi_enrichment_full: no visible global function definition for 'ppois'
Undefined global functions or variables:
abline dev.off download.file jpeg pdf plot ppois read.table sd
setTxtProgressBar tail txtProgressBar
Consider adding
importFrom("grDevices", "dev.off", "jpeg", "pdf")
importFrom("graphics", "abline", "plot")
importFrom("stats", "ppois", "sd")
importFrom("utils", "download.file", "read.table", "setTxtProgressBar",
"tail", "txtProgressBar")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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
'C:/Users/biocbuild/bbs-3.10-bioc/meat/STRINGdb.Rcheck/00check.log'
for details.
STRINGdb.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/STRINGdb_1.26.0.tar.gz && rm -rf STRINGdb.buildbin-libdir && mkdir STRINGdb.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STRINGdb.buildbin-libdir STRINGdb_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL STRINGdb_1.26.0.zip && rm STRINGdb_1.26.0.tar.gz STRINGdb_1.26.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
1 1066k 1 16384 0 0 499k 0 0:00:02 --:--:-- 0:00:02 551k
100 1066k 100 1066k 0 0 24.1M 0 --:--:-- --:--:-- --:--:-- 26.0M
install for i386
* installing *source* package 'STRINGdb' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'STRINGdb'
finding HTML links ... done
STRINGdb-class html
add_diff_exp_color html
add_proteins_description html
benchmark_ppi html
benchmark_ppi_pathway_view html
coeffOfvar html
delColDf html
diff_exp_example1 html
downloadAbsentFile html
downloadAbsentFileSTRING html
get_STRING_species html
get_aliases html
get_annotations html
get_annotations_desc html
get_bioc_graph html
get_clusters html
get_enrichment html
get_graph html
get_homologs html
get_homologs_besthits html
get_interactions html
get_link html
get_neighbors html
get_png html
get_ppi_enrichment html
get_ppi_enrichment_full html
get_proteins html
get_pubmed html
get_pubmed_interaction html
get_subnetwork html
get_summary html
get_term_proteins html
interactions html
load html
load_all html
map html
mp html
multi_map_df html
plot_network html
plot_ppi_enrichment html
plot_ppi_enrichment_graph html
post_payload html
ppi_enrichment html
ppi_enrichment_full html
ppie.compLambda html
ppie.compLambdaL1L2 html
ppie.compPij html
ppie.getNumEdgesBetween html
remove_homologous_interactions html
renameColDf html
set_background html
** 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
install for x64
* installing *source* package 'STRINGdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STRINGdb' as STRINGdb_1.26.0.zip
* DONE (STRINGdb)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'STRINGdb' successfully unpacked and MD5 sums checked
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STRINGdb.Rcheck/tests_i386/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> BiocGenerics:::testPackage("STRINGdb")
trying URL 'http://string.uzh.ch/permanent/string/10/protein_aliases/9606__protein_aliases_tf.tsv.gz'
Content type 'application/x-gzip' length 13939907 bytes (13.3 MB)
==================================================
downloaded 13.3 MB
trying URL 'http://string.uzh.ch/permanent/string/10/proteins/9606__proteins.tsv.gz'
Content type 'application/x-gzip' length 1815122 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
Warning: we couldn't map to STRING 14% of your identifiersWarning: we couldn't map to STRING 14% of your identifiers
RUNIT TEST PROTOCOL -- Wed Apr 15 07:02:02 2020
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
STRINGdb RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
203.90 5.42 224.37
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STRINGdb.Rcheck/tests_x64/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> BiocGenerics:::testPackage("STRINGdb")
trying URL 'http://string.uzh.ch/permanent/string/10/protein_aliases/9606__protein_aliases_tf.tsv.gz'
Content type 'application/x-gzip' length 13939907 bytes (13.3 MB)
==================================================
downloaded 13.3 MB
trying URL 'http://string.uzh.ch/permanent/string/10/proteins/9606__proteins.tsv.gz'
Content type 'application/x-gzip' length 1815122 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
Warning: we couldn't map to STRING 14% of your identifiersWarning: we couldn't map to STRING 14% of your identifiers
RUNIT TEST PROTOCOL -- Wed Apr 15 07:05:29 2020
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
STRINGdb RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
190.85 2.87 206.67
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STRINGdb.Rcheck/examples_i386/STRINGdb-Ex.timings
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STRINGdb.Rcheck/examples_x64/STRINGdb-Ex.timings
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