| Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:49:10 -0400 (Tue, 16 Apr 2019).
| Package 138/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] |  | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BiocInstaller |
| Version: 1.32.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BiocInstaller.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BiocInstaller_1.32.1.tar.gz |
| StartedAt: 2019-04-15 22:28:15 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:28:58 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 42.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocInstaller.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BiocInstaller.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BiocInstaller_1.32.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/BiocInstaller.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocInstaller/DESCRIPTION’ ... OK
* this is package ‘BiocInstaller’ version ‘1.32.1’
* 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 ‘BiocInstaller’ can be installed ... WARNING
Found the following significant warnings:
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See ‘/home/biocbuild/bbs-3.8-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
* 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 ... NOTE
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
package instead.
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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 ... 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 examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biocValid 9.672 0.18 11.262
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘BiocInstaller_unit_tests.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/BiocInstaller.Rcheck/00check.log’
for details.
BiocInstaller.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL BiocInstaller ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘BiocInstaller’ ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN package instead. Bioconductor version 3.8 (BiocInstaller 1.32.1), ?biocLite for help * DONE (BiocInstaller)
BiocInstaller.Rcheck/tests/BiocInstaller_unit_tests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("BiocInstaller")
Bioconductor version 3.8 (BiocInstaller 1.32.1), ?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
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
In addition: Warning message:
'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
package instead.
RUNIT TEST PROTOCOL -- Mon Apr 15 22:28:55 2019
***********************************************
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
1.236 0.064 2.252
BiocInstaller.Rcheck/BiocInstaller-Ex.timings
| name | user | system | elapsed | |
| BiocUpgrade | 0 | 0 | 0 | |
| biocLite | 0.028 | 0.000 | 0.040 | |
| biocUpdatePackages | 0 | 0 | 0 | |
| biocValid | 9.672 | 0.180 | 11.262 | |
| biocVersion | 0 | 0 | 0 | |
| biocinstallRepos | 0.004 | 0.000 | 0.003 | |
| packageGroups | 0.168 | 0.000 | 0.169 | |
| useDevel | 0 | 0 | 0 | |