Package: CTDquerier

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CTDquerier_1.6.0.tar.gz

StartedAt: 2020-04-15 01:33:15 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:36:34 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 198.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: CTDquerier.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CTDquerier_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CTDquerier.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CTDquerier/DESCRIPTION’ ... OK
* this is package ‘CTDquerier’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CTDquerier’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.1Mb
    extdata   4.1Mb
* 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
* 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 ... OK
* 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 ... WARNING
S4 class codoc mismatches from documentation object 'CTDdata':
Slots for class 'CTDdata'
  Code: chemicals_interactions diseases gene_gene_interactions
        gene_interactions go kegg losts terms timestamp type
  Docs: chemicals_interactions diseases gene_gene_interactions
        gene_interactions go kegg losts terms type

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'download_ctd_chem':
  ‘filename’ ‘mode’

Documented arguments not in \usage in documentation object 'download_ctd_dise':
  ‘filename’ ‘mode’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 176 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
query_ctd_gene 12.295  0.333  20.886
load_ctd_gene  12.266  0.274  12.674
query_ctd_chem  9.858  1.522  22.956
load_ctd_chem   5.059  0.135   5.253
query_ctd_dise  1.848  0.079  59.834
* 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: There's no line here to end.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
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* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE

Status: 1 ERROR, 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/CTDquerier.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CTDquerier
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CTDquerier’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (CTDquerier)

name	user	system	elapsed
download_ctd_chem	1.599	0.076	1.694
download_ctd_genes	0.177	0.002	0.183
gala	1.040	0.069	1.117
get_table-methods	0.709	0.036	0.752
get_terms-methods	0.749	0.036	0.792
leaf_plot	0.812	0.027	0.848
load_ctd_chem	5.059	0.135	5.253
load_ctd_dise	1.135	0.087	1.233
load_ctd_gene	12.266	0.274	12.674
query_ctd_chem	9.858	1.522	22.956
query_ctd_dise	1.848	0.079	59.834
query_ctd_gene	12.295	0.333	20.886