Martin Morgan
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Organism.dplyr |
| Branch: RELEASE_3_10 |
| Last Commit: 6121d67 |
| Last Changed Date: 2019-10-29 13:10:17 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:28:02 -0400 (Wed, 15 Apr 2020).
| Package 1201/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Organism.dplyr 1.14.0 Martin Morgan
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Organism.dplyr |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Organism.dplyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Organism.dplyr_1.14.0.tar.gz |
| StartedAt: 2020-04-15 05:16:36 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:26:34 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 597.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Organism.dplyr.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Organism.dplyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Organism.dplyr_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Organism.dplyr.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 'Organism.dplyr/DESCRIPTION' ... OK
* this is package 'Organism.dplyr' version '1.14.0'
* package encoding: UTF-8
* 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 'Organism.dplyr' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/filter.Rd:152: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/filter.Rd:155: file link 'select,src_organism-method' in package 'Organism.dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/select.Rd:137: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/src.Rd:130: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/src.Rd:133: file link 'select,src_organism-method' in package 'Organism.dplyr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Organism.dplyr.Rcheck/00install.out' for details.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
'AnnotationDbi:::smartKeys' 'GenomicFeatures:::.exons_with_3utr'
'GenomicFeatures:::.exons_with_5utr'
'GenomicFeatures:::get_TxDb_seqinfo0'
'S4Vectors:::extract_data_frame_rows'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.toGRanges: no visible binding for global variable '.'
intronsByTranscript,src_organism: no visible binding for global
variable '.'
orgPackageName,src_organism: no visible binding for global variable
'name'
orgPackageName,src_organism: no visible binding for global variable
'organism'
orgPackageName,src_organism: no visible binding for global variable
'OrgDb'
Undefined global functions or variables:
. OrgDb name organism
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Genomic-Extractors 4.91 0.36 5.59
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/Organism.dplyr.Rcheck/00check.log'
for details.
Organism.dplyr.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/Organism.dplyr_1.14.0.tar.gz && rm -rf Organism.dplyr.buildbin-libdir && mkdir Organism.dplyr.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Organism.dplyr.buildbin-libdir Organism.dplyr_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Organism.dplyr_1.14.0.zip && rm Organism.dplyr_1.14.0.tar.gz Organism.dplyr_1.14.0.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
0 200k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 200k 100 200k 0 0 1358k 0 --:--:-- --:--:-- --:--:-- 1384k
install for i386
* installing *source* package 'Organism.dplyr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Organism.dplyr'
finding HTML links ... done
Genomic-Extractors html
finding level-2 HTML links ... done
filter html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/filter.Rd:152: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/filter.Rd:155: file link 'select,src_organism-method' in package 'Organism.dplyr' does not exist and so has been treated as a topic
select html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/select.Rd:137: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
src html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/src.Rd:130: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMNlkXU/R.INSTALL8843c06e24/Organism.dplyr/man/src.Rd:133: file link 'select,src_organism-method' in package 'Organism.dplyr' does not exist and so has been treated as a topic
utils 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 'Organism.dplyr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Organism.dplyr' as Organism.dplyr_1.14.0.zip
* DONE (Organism.dplyr)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Organism.dplyr' successfully unpacked and MD5 sums checked
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Organism.dplyr.Rcheck/tests_i386/testthat.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.
> library(testthat)
> library(Organism.dplyr)
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: AnnotationFilter
Attaching package: 'AnnotationFilter'
The following object is masked from 'package:testthat':
not
>
> test_check("Organism.dplyr")
== testthat results ===========================================================
[ OK: 190 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
110.82 5.43 174.62
|
Organism.dplyr.Rcheck/tests_x64/testthat.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.
> library(testthat)
> library(Organism.dplyr)
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: AnnotationFilter
Attaching package: 'AnnotationFilter'
The following object is masked from 'package:testthat':
not
>
> test_check("Organism.dplyr")
== testthat results ===========================================================
[ OK: 190 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
105.62 4.35 109.98
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Organism.dplyr.Rcheck/examples_i386/Organism.dplyr-Ex.timings
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Organism.dplyr.Rcheck/examples_x64/Organism.dplyr-Ex.timings
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