Iain Wallace
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/bgafun |
| Branch: RELEASE_3_9 |
| Last Commit: 0e02f64 |
| Last Changed Date: 2019-05-02 11:53:08 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:21:29 -0400 (Wed, 16 Oct 2019).
| Package 127/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bgafun 1.46.0 Iain Wallace
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: bgafun |
| Version: 1.46.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bgafun.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings bgafun_1.46.0.tar.gz |
| StartedAt: 2019-10-16 02:08:57 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:10:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 72.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bgafun.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bgafun.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings bgafun_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/bgafun.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bgafun/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bgafun' version '1.46.0'
* 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 'bgafun' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
'ade4' 'made4' 'seqinr'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
run_between_pca: no visible global function definition for 'dudi.pca'
run_between_pca: no visible global function definition for 'bca'
Undefined global functions or variables:
bca dudi.pca
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
add_pseudo_counts 6.73 0 6.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
add_pseudo_counts 11.11 0.02 11.12
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/bgafun.Rcheck/00check.log'
for details.
bgafun.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bgafun_1.46.0.tar.gz && rm -rf bgafun.buildbin-libdir && mkdir bgafun.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bgafun.buildbin-libdir bgafun_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bgafun_1.46.0.zip && rm bgafun_1.46.0.tar.gz bgafun_1.46.0.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
100 157k 100 157k 0 0 1073k 0 --:--:-- --:--:-- --:--:-- 1126k
install for i386
* installing *source* package 'bgafun' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'bgafun'
finding HTML links ... done
Calculate_Row_Weights html
Henikoff_weights html
LDH html
LDH.aap html
LDH.aap.ave html
LDH.amino html
LDH.amino.gapless html
LDH.amino.pseudo html
LDH.groups html
Weight_Amino html
add_pseudo_counts html
amino_counts html
average_cols_aap html
bgafun html
calculate_pseudo html
convertAAP.package html
convert_aln_AAP html
convert_aln_amino html
convert_amino.package html
convert_seq_AAP html
convert_seq_amino html
create_colnames_AAP html
create_colnames_amino html
create_probab html
create_profile html
create_profile_strings html
pseudo_counts html
remove_gaps html
remove_gaps_groups html
run_between_pca html
sum_20_aln html
sum_20_cols html
sum_aln html
top_residues_2_groups 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 'bgafun' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bgafun' as bgafun_1.46.0.zip
* DONE (bgafun)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'bgafun' successfully unpacked and MD5 sums checked
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bgafun.Rcheck/examples_i386/bgafun-Ex.timings
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bgafun.Rcheck/examples_x64/bgafun-Ex.timings
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