| Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:35:23 -0400 (Wed, 17 Oct 2018).
| Package 130/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocInstaller 1.30.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BiocInstaller |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocInstaller.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BiocInstaller_1.30.0.tar.gz |
| StartedAt: 2018-10-17 00:44:24 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:45:12 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 48.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocInstaller.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocInstaller.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BiocInstaller_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/BiocInstaller.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocInstaller/DESCRIPTION' ... OK
* this is package 'BiocInstaller' version '1.30.0'
* 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 'BiocInstaller' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpo9MMbP/R.INSTALLcec40c957d9/BiocInstaller/man/biocLite.Rd:73: missing file link 'install'
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/BiocInstaller.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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 ... NOTE
'library' or 'require' call to 'utils' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'utils:::.clean_up_dependencies'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.updateBiocInstallerFinish' '.updateFinish'
* 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 ... WARNING
Missing link or links in documentation object 'biocLite.Rd':
'[remotes]{install}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biocValid 7.08 1.05 8.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biocValid 6.33 0.95 7.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'BiocInstaller_unit_tests.R'
OK
** running tests for arch 'x64' ...
Running 'BiocInstaller_unit_tests.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/BiocInstaller.Rcheck/00check.log'
for details.
BiocInstaller.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/BiocInstaller_1.30.0.tar.gz && rm -rf BiocInstaller.buildbin-libdir && mkdir BiocInstaller.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocInstaller.buildbin-libdir BiocInstaller_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL BiocInstaller_1.30.0.zip && rm BiocInstaller_1.30.0.tar.gz BiocInstaller_1.30.0.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 19291 100 19291 0 0 360k 0 --:--:-- --:--:-- --:--:-- 418k
install for i386
* installing *source* package 'BiocInstaller' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BiocInstaller'
finding HTML links ... done
BiocUpgrade html
biocLite html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpo9MMbP/R.INSTALLcec40c957d9/BiocInstaller/man/biocLite.Rd:73: missing file link 'install'
biocUpdatePackages html
biocValid html
biocVersion html
biocinstallRepos html
packageGroups html
useDevel html
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
In R CMD INSTALL
install for x64
* installing *source* package 'BiocInstaller' ...
** testing if installed package can be loaded
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
* MD5 sums
packaged installation of 'BiocInstaller' as BiocInstaller_1.30.0.zip
* DONE (BiocInstaller)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'BiocInstaller' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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BiocInstaller.Rcheck/tests_i386/BiocInstaller_unit_tests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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("BiocInstaller")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
installation path not writeable, unable to update packages: Foo
installation path not writeable, unable to update packages: Foo
installation path not writeable, unable to update packages: Bar
installation path not writeable, unable to update packages: Foo, Bar, Baz
Timing stopped at: 0 0 0
Error in DEACTIVATED("too idiosyncratic for standardized testing") :
too idiosyncratic for standardized testing
RUNIT TEST PROTOCOL -- Wed Oct 17 00:45:06 2018
***********************************************
Number of test functions: 10
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocInstaller RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
0.95 0.15 1.62
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BiocInstaller.Rcheck/tests_x64/BiocInstaller_unit_tests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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("BiocInstaller")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
installation path not writeable, unable to update packages: Foo
installation path not writeable, unable to update packages: Foo
installation path not writeable, unable to update packages: Bar
installation path not writeable, unable to update packages: Foo, Bar, Baz
Timing stopped at: 0 0 0
Error in DEACTIVATED("too idiosyncratic for standardized testing") :
too idiosyncratic for standardized testing
RUNIT TEST PROTOCOL -- Wed Oct 17 00:45:08 2018
***********************************************
Number of test functions: 10
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocInstaller RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
1.07 0.12 1.40
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BiocInstaller.Rcheck/examples_i386/BiocInstaller-Ex.timings
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BiocInstaller.Rcheck/examples_x64/BiocInstaller-Ex.timings
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