Martin Morgan
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/Organism.dplyr |
| Branch: RELEASE_3_6 |
| Last Commit: 1e1707a |
| Last Changed Date: 2018-01-09 13:35:05 -0400 (Tue, 09 Jan 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:29:27 -0400 (Thu, 12 Apr 2018).
| Package 984/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Organism.dplyr 1.6.2 Martin Morgan
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ ERROR ] | OK | |||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: Organism.dplyr |
| Version: 1.6.2 |
| Command: rm -rf Organism.dplyr.buildbin-libdir Organism.dplyr.Rcheck && mkdir Organism.dplyr.buildbin-libdir Organism.dplyr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Organism.dplyr.buildbin-libdir Organism.dplyr_1.6.2.tar.gz >Organism.dplyr.Rcheck\00install.out 2>&1 && cp Organism.dplyr.Rcheck\00install.out Organism.dplyr-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Organism.dplyr.buildbin-libdir --install="check:Organism.dplyr-install.out" --force-multiarch --no-vignettes --timings Organism.dplyr_1.6.2.tar.gz |
| StartedAt: 2018-04-12 01:57:18 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:07:00 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 582.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Organism.dplyr.Rcheck |
| Warnings: NA |
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### Running command:
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### rm -rf Organism.dplyr.buildbin-libdir Organism.dplyr.Rcheck && mkdir Organism.dplyr.buildbin-libdir Organism.dplyr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Organism.dplyr.buildbin-libdir Organism.dplyr_1.6.2.tar.gz >Organism.dplyr.Rcheck\00install.out 2>&1 && cp Organism.dplyr.Rcheck\00install.out Organism.dplyr-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Organism.dplyr.buildbin-libdir --install="check:Organism.dplyr-install.out" --force-multiarch --no-vignettes --timings Organism.dplyr_1.6.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Organism.dplyr.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.6.2'
* 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-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/filter.Rd:152: missing file link 'transcripts_tbl'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/filter.Rd:155: missing file link 'select,src_organism-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/select.Rd:137: missing file link 'transcripts_tbl'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/src.Rd:123: missing file link 'transcripts_tbl'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/src.Rd:126: missing file link 'select,src_organism-method'
See 'C:/Users/biocbuild/bbs-3.6-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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Genomic-Extractors 5.82 0.04 5.86
* 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'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
27: dbFetch(qry, 0)
28: dbFetch(qry, 0)
29: .local(res, n, ...)
30: sqlColumnToRownames(result_fetch(res@ptr, n = n), row.names)
31: result_fetch(res@ptr, n = n)
== testthat results ===========================================================
OK: 200 SKIPPED: 0 FAILED: 1
1. Error: cds-extractor (@test-GenomicFeatures-extractors.R#161)
Error: testthat unit tests failed
In addition: Warning messages:
1: Closing open result set, pending rows
2: call dbDisconnect() when finished working with a connection
Execution halted
* 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 ERROR, 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/Organism.dplyr.Rcheck/00check.log'
for details.
Organism.dplyr.Rcheck/00install.out
install for i386
* installing *source* package 'Organism.dplyr' ...
** R
** inst
** preparing 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-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/filter.Rd:152: missing file link 'transcripts_tbl'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/filter.Rd:155: missing file link 'select,src_organism-method'
select html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/select.Rd:137: missing file link 'transcripts_tbl'
src html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/src.Rd:123: missing file link 'transcripts_tbl'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpem2R68/R.INSTALL254c2c6a410d/Organism.dplyr/man/src.Rd:126: missing file link 'select,src_organism-method'
utils html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
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_1.6.2.zip
* DONE (Organism.dplyr)
In R CMD INSTALL
In R CMD INSTALL
|
Organism.dplyr.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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.
> 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: 201 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
88.45 3.45 179.90
|
Organism.dplyr.Rcheck/tests_x64/testthat.Rout.fail
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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.
> 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")
-- 1. Error: cds-extractor (@test-GenomicFeatures-extractors.R#161) -----------
Invalid result set
1: .test_extractor_egfilter(src, txdb, cds, "cds_id") at testthat/test-GenomicFeatures-extractors.R:161
2: fun(src0, filter = ˜!(symbol != "ADA") & tx_id != 169786) at testthat/test-GenomicFeatures-extractors.R:66
3: fun(src0, filter = ˜!(symbol != "ADA") & tx_id != 169786)
4: .local(x, ...)
5: .toGRanges(x, .xscripts_tbl(x, "ranges_cds", filter), filter)
6: table %>% filter_at(vars(c(1, 2, 3, 4)), all_vars(!is.na(.)))
7: eval(lhs, parent, parent)
8: eval(lhs, parent, parent)
9: .xscripts_tbl(x, "ranges_cds", filter)
10: .xscripts(x, main_ranges, filter)
...
22: tbl(dbplyr::src_dbi(src), from = from, ...)
23: tbl.src_dbi(dbplyr::src_dbi(src), from = from, ...)
24: tbl_sql("dbi", src = src, from = from)
25: db_query_fields(src$con, from)
26: db_query_fields.DBIConnection(src$con, from)
27: dbFetch(qry, 0)
28: dbFetch(qry, 0)
29: .local(res, n, ...)
30: sqlColumnToRownames(result_fetch(res@ptr, n = n), row.names)
31: result_fetch(res@ptr, n = n)
== testthat results ===========================================================
OK: 200 SKIPPED: 0 FAILED: 1
1. Error: cds-extractor (@test-GenomicFeatures-extractors.R#161)
Error: testthat unit tests failed
In addition: Warning messages:
1: Closing open result set, pending rows
2: call dbDisconnect() when finished working with a connection
Execution halted
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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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