Multiple platform build/check report for BioC 3.10 - CHECK report for CTDquerier on tokay1

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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:CTDquerier.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CTDquerier_1.6.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CTDquerier.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 '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 whether package 'CTDquerier' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.6Mb
  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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
load_ctd_gene  12.34   0.73   13.08
query_ctd_chem 11.27   1.08   29.64
query_ctd_gene  8.90   0.73   16.30
load_ctd_chem   5.06   0.25    5.33
query_ctd_dise  1.11   0.05   48.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
load_ctd_gene  10.43   0.28   10.72
query_ctd_gene 10.34   0.20   16.71
query_ctd_chem  8.00   0.15   21.42
load_ctd_chem   5.67   0.13    5.80
query_ctd_dise  1.41   0.02   49.71
* 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.
 ...                                              
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE

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

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CTDquerier_1.6.0.tar.gz && rm -rf CTDquerier.buildbin-libdir && mkdir CTDquerier.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CTDquerier.buildbin-libdir CTDquerier_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CTDquerier_1.6.0.zip && rm CTDquerier_1.6.0.tar.gz CTDquerier_1.6.0.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 3720k  100 3720k    0     0  43.1M      0 --:--:-- --:--:-- --:--:-- 44.8M

install for i386

* 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
  converting help for package 'CTDquerier'
    finding HTML links ... done
    CTDdata-class                           html  
    CTDquerier                              html  
    download_ctd_chem                       html  
    download_ctd_dise                       html  
    download_ctd_genes                      html  
    enrich-methods                          html  
    gala                                    html  
    get_table-methods                       html  
    get_terms-methods                       html  
    leaf_plot                               html  
    load_ctd_chem                           html  
    load_ctd_dise                           html  
    load_ctd_gene                           html  
    query_ctd_chem                          html  
    query_ctd_dise                          html  
    query_ctd_gene                          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 'CTDquerier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CTDquerier' as CTDquerier_1.6.0.zip
* DONE (CTDquerier)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CTDquerier' successfully unpacked and MD5 sums checked

CHECK report for CTDquerier on tokay1

Summary

Command output

Installation output

Tests output

Example timings