| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:26 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the STRINGdb package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/STRINGdb.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 1892/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| STRINGdb 2.6.5 (landing page) Damian Szklarczyk
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: STRINGdb |
| Version: 2.6.5 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STRINGdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings STRINGdb_2.6.5.tar.gz |
| StartedAt: 2022-04-13 03:39:16 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 03:47:56 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 519.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: STRINGdb.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STRINGdb.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings STRINGdb_2.6.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/STRINGdb.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.6.5'
* 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'
Undefined global functions or variables:
download.file read.table sd tail
Consider adding
importFrom("stats", "sd")
importFrom("utils", "download.file", "read.table", "tail")
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-3.14-bioc/meat/STRINGdb.Rcheck/00check.log'
for details.
STRINGdb.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/STRINGdb_2.6.5.tar.gz && rm -rf STRINGdb.buildbin-libdir && mkdir STRINGdb.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STRINGdb.buildbin-libdir STRINGdb_2.6.5.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL STRINGdb_2.6.5.zip && rm STRINGdb_2.6.5.tar.gz STRINGdb_2.6.5.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
100 941k 100 941k 0 0 1565k 0 --:--:-- --:--:-- --:--:-- 1569k
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
coeffOfvar html
delColDf html
diff_exp_example1 html
downloadAbsentFile html
downloadAbsentFileSTRING 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_besthits html
get_interactions html
get_link html
get_neighbors html
get_paralogs html
get_png html
get_ppi_enrichment html
get_proteins 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
post_payload 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_2.6.5.zip
* DONE (STRINGdb)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'STRINGdb' successfully unpacked and MD5 sums checked
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STRINGdb.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 'https://stringdb-static.org/download/protein.aliases.v11.0/9606.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 13253303 bytes (12.6 MB)
==================================================
downloaded 12.6 MB
trying URL 'https://stringdb-static.org/download/protein.info.v11.0/9606.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 1894048 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://stringdb-static.org/download/protein.info.v11.0/511145.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 276124 bytes (269 KB)
==================================================
downloaded 269 KB
trying URL 'https://stringdb-static.org/download/protein.links.v11.0/511145.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 5323410 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
Warning: we couldn't map to STRING 15% of your identifierstrying URL 'https://stringdb-static.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 71241372 bytes (67.9 MB)
==================================================
downloaded 67.9 MB
RUNIT TEST PROTOCOL -- Wed Apr 13 03:44:12 2022
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
STRINGdb RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
212.73 6.31 239.17
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STRINGdb.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
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.
> BiocGenerics:::testPackage("STRINGdb")
trying URL 'https://stringdb-static.org/download/protein.aliases.v11.0/9606.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 13253303 bytes (12.6 MB)
==================================================
downloaded 12.6 MB
trying URL 'https://stringdb-static.org/download/protein.info.v11.0/9606.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 1894048 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://stringdb-static.org/download/protein.info.v11.0/511145.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 276124 bytes (269 KB)
==================================================
downloaded 269 KB
trying URL 'https://stringdb-static.org/download/protein.links.v11.0/511145.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 5323410 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
Warning: we couldn't map to STRING 15% of your identifierstrying URL 'https://stringdb-static.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 71241372 bytes (67.9 MB)
==================================================
downloaded 67.9 MB
RUNIT TEST PROTOCOL -- Wed Apr 13 03:47:47 2022
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
STRINGdb RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
194.81 2.14 214.68
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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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