##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterMineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings InterMineR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/InterMineR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'InterMineR/DESCRIPTION' ... OK
* this is package 'InterMineR' version '1.16.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'InterMineR' can be installed ... WARNING
Found the following significant warnings:
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
  Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
  Warning: multiple methods tables found for 'union'
  Warning: multiple methods tables found for 'intersect'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/InterMineR.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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Warning: multiple methods tables found for 'union'
Warning: multiple methods tables found for 'intersect'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: multiple methods tables found for 'union'
Warning: multiple methods tables found for 'intersect'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
convertToGeneAnswers: no visible binding for global variable
  'geneExpProfile'
convertToRangedSummarizedExperiment: no visible global function
  definition for 'reshape'
listDatasets: no visible binding for global variable 'child_name'
create_list,ListManager: no visible global function definition for
  'URLencode'
doEnrichment,Service: no visible global function definition for
  'URLencode'
do_operation,ListManager: no visible global function definition for
  'URLencode'
runQuery,ANY-InterMineR: no visible global function definition for
  'URLencode'
runQuery,ANY-list: no visible global function definition for
  'URLencode'
subtract,ListManager: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode child_name geneExpProfile reshape
Consider adding
  importFrom("stats", "reshape")
  importFrom("utils", "URLencode")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: man/ListManager-methods.Rd:41: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:42: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:50: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:51: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:59: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:60: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:63: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:66: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:69: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:72: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:80: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:81: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:84: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:87: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:90: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:98: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:99: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:102: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:105: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:108: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:116: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:117: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:120: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:123: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:126: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:134: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:135: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:138: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:141: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:144: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:147: unknown macro '\item'
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'webservice-methods':
  'doEnrichment.Rd' 'list_manager.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'GET_api_list' 'get_unused_list_name'
Undocumented S4 classes:
  'Service'
Undocumented S4 methods:
  generic 'GET_api_list' and siglist 'ListManager'
  generic 'doEnrichment' and siglist 'Service'
  generic 'get_unused_list_name' and siglist 'ListManager'
  generic 'list_manager' and siglist 'Service'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'doEnrichment':
doEnrichment
  Code: function(object, ...)
  Docs: function(- Service class, genelist = NULL, ids = NULL, widget =
                 NULL, population = NULL, maxp = 0.05, correction =
                 "Benjamini Hochberg", filter = NULL, organism = NULL)
  Argument names in code not in docs:
    object ...
  Argument names in docs not in code:
    - Service class genelist ids widget population maxp correction
    filter organism
  Mismatches in argument names:
    Position: 1 Code: object Docs: - Service class
    Position: 2 Code: ... Docs: genelist

Codoc mismatches from documentation object 'list_manager':
list_manager
  Code: function(object, ...)
  Docs: function(- Service class)
  Argument names in code not in docs:
    object ...
  Argument names in docs not in code:
    - Service class
  Mismatches in argument names:
    Position: 1 Code: object Docs: - Service class

S4 class codoc mismatches from documentation object 'ListManager-class':
Slots for class 'ListManager'
  Code: DEFAULT_DESCRIPTION DEFAULT_LIST_NAME DIFFERENCE_PATH
        INTERSECTION_PATH LIST_PATH SUBTRACTION_PATH UNION_PATH mine
        token
  Docs: DEFAULT_DESCRIPTION DEFAULT_LIST_NAME DIFFERENCE_PATH
        INTERSECTION_PATH LIST_PATH SUBTRACTION_PATH UNION_PATH mine
        name token

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'doEnrichment'
  'Service - class'
Documented arguments not in \usage in documentation object 'doEnrichment':
  'Service-class'

Undocumented arguments in documentation object 'list_manager'
  'Service - class'
Documented arguments not in \usage in documentation object 'list_manager':
  'Service-class'

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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'InterMineR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: InterMineR-methods
> ### Title: Methods for accessing 'InterMineR-class' objects.
> ### Aliases: InterMineR-methods getName getName-methods
> ###   getName,InterMineR-method getDescription getDescription-methods
> ###   getDescription,InterMineR-method getSelect getSelect-methods
> ###   getSelect,InterMineR-method getOrderBy getOrderBy-methods
> ###   getOrderBy,InterMineR-method getWhere getWhere-methods
> ###   getWhere,InterMineR-method
> 
> ### ** Examples
> 
> # get mine instance
> im.fly = initInterMine(listMines()["FlyMine"])
> 
> # get GO_Gene template query
> qGO_Gene = getTemplateQuery(im.fly, "GO_Gene")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  schannel: next InitializeSecurityContext failed: SEC_E_MESSAGE_ALTERED (0x8009030F) - The message or signature supplied for verification has been altered
Calls: getTemplateQuery ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
simplifyResult                      8.52   0.06   12.99
convertToRangedSummarizedExperiment 3.89   0.02    9.14
runQuery                            3.01   0.02    5.75
* 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, 6 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/InterMineR.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/InterMineR_1.16.0.tar.gz && rm -rf InterMineR.buildbin-libdir && mkdir InterMineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InterMineR.buildbin-libdir InterMineR_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL InterMineR_1.16.0.zip && rm InterMineR_1.16.0.tar.gz InterMineR_1.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  2 4506k    2 97081    0     0   399k      0  0:00:11 --:--:--  0:00:11  400k
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 71 4506k   71 3233k    0     0  1457k      0  0:00:03  0:00:02  0:00:01 1457k
100 4506k  100 4506k    0     0  1601k      0  0:00:02  0:00:02 --:--:-- 1601k

install for i386

* installing *source* package 'InterMineR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'intersect' in package 'InterMineR'
Creating a new generic function for 'union' in package 'InterMineR'
** help
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCupX1U/R.INSTALL1db85ac34efa/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
*** installing help indices
  converting help for package 'InterMineR'
    finding HTML links ... done
    InterMineR-class                        html  
    InterMineR-methods                      html  
    InterMineR-package                      html  
    ListManager-class                       html  
    ListManager-methods                     html  
    PL_DiabetesGenes                        html  
    PL_FlyTF_site_specific_TFs              html  
    convertToGRanges                        html  
    convertToGeneAnswers                    html  
    convertToRangedSummarizedExperiment     html  
    doEnrichment                            html  
    getDatasets                             html  
    getGeneIds                              html  
    getModel                                html  
    getRelease                              html  
    getTemplateQuery                        html  
    getTemplates                            html  
    getVersion                              html  
    getWidgets                              html  
    initInterMine                           html  
    listDatasets                            html  
    listMines                               html  
    list_manager                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/InterMineR.buildbin-libdir/00LOCK-InterMineR/00new/InterMineR/help/webservice-methods.html
    newQuery                                html  
    runQuery                                html  
    setConstraints                          html  
    setQuery                                html  
    simplifyResult                          html  
    summary                                 html  
    webservice-class                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for 'union'
Warning: multiple methods tables found for 'intersect'
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for 'union'
Warning: multiple methods tables found for 'intersect'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'InterMineR' ...
** testing if installed package can be loaded
Warning: multiple methods tables found for 'union'
Warning: multiple methods tables found for 'intersect'
* MD5 sums
packaged installation of 'InterMineR' as InterMineR_1.16.0.zip
* DONE (InterMineR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'InterMineR' successfully unpacked and MD5 sums checked