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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CTDquerier.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CTDquerier_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CTDquerier.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.8.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'CTDquerier' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CTDquerier.Rcheck/00install.out' for details.
* 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 (user + system) or elapsed time > 5s
                user system elapsed
load_ctd_gene  11.92   0.47   14.17
query_ctd_gene 10.24   0.67   19.31
query_ctd_chem  8.80   0.36   24.36
load_ctd_chem   5.23   0.23    6.12
query_ctd_dise  1.87   0.05   56.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
query_ctd_gene 12.66   0.29   35.90
load_ctd_gene  12.78   0.12   12.90
query_ctd_chem  7.44   0.14   23.72
query_ctd_dise  1.90   0.10   36.05
* 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, 4 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/CTDquerier.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CTDquerier_1.8.0.tar.gz && rm -rf CTDquerier.buildbin-libdir && mkdir CTDquerier.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CTDquerier.buildbin-libdir CTDquerier_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CTDquerier_1.8.0.zip && rm CTDquerier_1.8.0.tar.gz CTDquerier_1.8.0.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 3717k  100 3717k    0     0  17.9M      0 --:--:-- --:--:-- --:--:-- 18.6M

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
Warning: Package 'CTDquerier' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'CTDquerier' is deprecated and will be removed from
  Bioconductor version 3.12
** 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
Warning: Package 'CTDquerier' is deprecated and will be removed from
  Bioconductor version 3.12
* MD5 sums
packaged installation of 'CTDquerier' as CTDquerier_1.8.0.zip
* DONE (CTDquerier)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CTDquerier' successfully unpacked and MD5 sums checked