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This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1051/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InterMineR 1.26.0  (landing page)
InterMine Team
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/InterMineR
git_branch: RELEASE_3_19
git_last_commit: 7d319ce
git_last_commit_date: 2024-04-30 11:00:23 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for InterMineR on merida1

To the developers/maintainers of the InterMineR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/InterMineR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: InterMineR
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings InterMineR_1.26.0.tar.gz
StartedAt: 2024-10-17 07:02:42 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 07:10:20 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 458.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: InterMineR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings InterMineR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* this is package ‘InterMineR’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘InterMineR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
  Warning: multiple methods tables found for ‘union’
  Warning: multiple methods tables found for ‘subtract’
  Warning: multiple methods tables found for ‘intersect’
See ‘/Users/biocbuild/bbs-3.19-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 code 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 ... NOTE
Warning: multiple methods tables found for ‘union’
Warning: multiple methods tables found for ‘subtract’
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 whether startup messages can be suppressed ... 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
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 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'
checkRd: (-1) ListManager-methods.Rd:41-45: Lost braces
    41 |       \arguments{
       |                 ^
checkRd: (-1) ListManager-methods.Rd:42: Lost braces
    42 |         \item{list_name}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:42-44: Lost braces
    42 |         \item{list_name}{
       |                         ^
checkRd: (-1) ListManager-methods.Rd:50-54: Lost braces
    50 |       \arguments{
       |                 ^
checkRd: (-1) ListManager-methods.Rd:51: Lost braces
    51 |         \item{lists}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:51-53: Lost braces
    51 |         \item{lists}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:59-75: Lost braces
    59 |       \arguments{
       |                 ^
checkRd: (-1) ListManager-methods.Rd:60: Lost braces
    60 |         \item{content}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:60-62: Lost braces
    60 |         \item{content}{
       |                       ^
checkRd: (-1) ListManager-methods.Rd:63: Lost braces
    63 |         \item{list_type}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:63-65: Lost braces
    63 |         \item{list_type}{
       |                         ^
checkRd: (-1) ListManager-methods.Rd:66: Lost braces
    66 |          \item{name}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:66-68: Lost braces
    66 |          \item{name}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:69: Lost braces
    69 |          \item{description}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:69-71: Lost braces
    69 |          \item{description}{
       |                            ^
checkRd: (-1) ListManager-methods.Rd:72: Lost braces
    72 |         \item{organism}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:72-74: Lost braces
    72 |         \item{organism}{
       |                        ^
checkRd: (-1) ListManager-methods.Rd:80-93: Lost braces
    80 |       \arguments{
       |                 ^
checkRd: (-1) ListManager-methods.Rd:81: Lost braces
    81 |         \item{lists}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:81-83: Lost braces
    81 |         \item{lists}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:84: Lost braces
    84 |          \item{name}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:84-86: Lost braces
    84 |          \item{name}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:87: Lost braces
    87 |          \item{description}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:87-89: Lost braces
    87 |          \item{description}{
       |                            ^
checkRd: (-1) ListManager-methods.Rd:90: Lost braces
    90 |         \item{tags}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:90-92: Lost braces
    90 |         \item{tags}{
       |                    ^
checkRd: (-1) ListManager-methods.Rd:98-111: Lost braces
    98 |       \arguments{
       |                 ^
checkRd: (-1) ListManager-methods.Rd:99: Lost braces
    99 |         \item{lists}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:99-101: Lost braces
    99 |         \item{lists}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:102: Lost braces
   102 |          \item{name}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:102-104: Lost braces
   102 |          \item{name}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:105: Lost braces
   105 |          \item{description}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:105-107: Lost braces
   105 |          \item{description}{
       |                            ^
checkRd: (-1) ListManager-methods.Rd:108: Lost braces
   108 |         \item{tags}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:108-110: Lost braces
   108 |         \item{tags}{
       |                    ^
checkRd: (-1) ListManager-methods.Rd:116-129: Lost braces
   116 |       \arguments{
       |                 ^
checkRd: (-1) ListManager-methods.Rd:117: Lost braces
   117 |         \item{lists}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:117-119: Lost braces
   117 |         \item{lists}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:120: Lost braces
   120 |          \item{name}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:120-122: Lost braces
   120 |          \item{name}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:123: Lost braces
   123 |          \item{description}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:123-125: Lost braces
   123 |          \item{description}{
       |                            ^
checkRd: (-1) ListManager-methods.Rd:126: Lost braces
   126 |         \item{tags}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:126-128: Lost braces
   126 |         \item{tags}{
       |                    ^
checkRd: (-1) ListManager-methods.Rd:134-150: Lost braces
   134 |        \arguments{
       |                  ^
checkRd: (-1) ListManager-methods.Rd:135: Lost braces
   135 |         \item{lefts}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:135-137: Lost braces
   135 |         \item{lefts}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:138: Lost braces
   138 |         \item{rights}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:138-140: Lost braces
   138 |         \item{rights}{
       |                      ^
checkRd: (-1) ListManager-methods.Rd:141: Lost braces
   141 |          \item{name}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:141-143: Lost braces
   141 |          \item{name}{
       |                     ^
checkRd: (-1) ListManager-methods.Rd:144: Lost braces
   144 |          \item{description}{
       |               ^
checkRd: (-1) ListManager-methods.Rd:144-146: Lost braces
   144 |          \item{description}{
       |                            ^
checkRd: (-1) ListManager-methods.Rd:147: Lost braces
   147 |         \item{tags}{
       |              ^
checkRd: (-1) ListManager-methods.Rd:147-149: Lost braces
   147 |         \item{tags}{
       |                    ^
checkRd: (-1) initInterMine.Rd:26: Lost braces
    26 | /url{http://intermine.readthedocs.io/en/latest/web-services/}
       |     ^
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'webservice-methods':
  ‘doEnrichment.Rd’ ‘list_manager.Rd’
* checking Rd cross-references ... NOTE
Unknown package ‘GeneAnswers’ in Rd xrefs
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘GET_api_list’ ‘do_operation’ ‘get_unused_list_name’
Undocumented S4 classes:
  ‘Service’
Undocumented S4 methods:
  generic 'GET_api_list' and siglist 'ListManager'
  generic 'doEnrichment' and siglist 'Service'
  generic 'do_operation' and siglist 'ListManager'
  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
Functions or methods with usage in Rd file 'convertToGeneAnswers.Rd' but not in code:
  ‘convertToGeneAnswers’

Codoc mismatches from Rd file 'doEnrichment.Rd':
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 Rd file 'list_manager.Rd':
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 Rd file 'ListManager-class.Rd':
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 Rd file 'doEnrichment.Rd'
  ‘Service - class’
Documented arguments not in \usage in Rd file 'doEnrichment.Rd':
  ‘Service-class’

Undocumented arguments in Rd file 'list_manager.Rd'
  ‘Service - class’
Documented arguments not in \usage in Rd file 'list_manager.Rd':
  ‘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 ... 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) : 
  Could not resolve host: NA
Calls: getTemplateQuery ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck/00check.log’
for details.


Installation output

InterMineR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL InterMineR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* 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’
Creating a new generic function for ‘subtract’ in package ‘InterMineR’
** help
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
*** installing help indices
** 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 ‘subtract’
Warning: multiple methods tables found for ‘intersect’
Warning in fun(libname, pkgname) :
  Package 'InterMineR' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘union’
Warning: multiple methods tables found for ‘subtract’
Warning: multiple methods tables found for ‘intersect’
Warning in fun(libname, pkgname) :
  Package 'InterMineR' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (InterMineR)

Tests output


Example timings

InterMineR.Rcheck/InterMineR-Ex.timings

nameusersystemelapsed