InterMine Team
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/InterMineR |
| git_branch: RELEASE_3_18 |
| git_last_commit: 44aa2fd |
| git_last_commit_date: 2023-10-24 10:59:29 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:12 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1037/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| InterMineR 1.24.0 (landing page) InterMine Team
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the InterMineR package: - 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. |
| Package: InterMineR |
| Version: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2024-04-17 17:11:05 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 17:15:04 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 239.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: InterMineR.Rcheck |
| Warnings: 6 |
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### Running command:
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### /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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/InterMineR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* this is package ‘InterMineR’ version ‘1.24.0’
* 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: ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:42: unknown macro '\item'
Warning: ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:51: unknown macro '\item'
Warning: ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:60: unknown macro '\item'
Warning: ListManager-methods.Rd:63: unknown macro '\item'
Warning: ListManager-methods.Rd:66: unknown macro '\item'
Warning: ListManager-methods.Rd:69: unknown macro '\item'
Warning: ListManager-methods.Rd:72: unknown macro '\item'
Warning: ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:81: unknown macro '\item'
Warning: ListManager-methods.Rd:84: unknown macro '\item'
Warning: ListManager-methods.Rd:87: unknown macro '\item'
Warning: ListManager-methods.Rd:90: unknown macro '\item'
Warning: ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:99: unknown macro '\item'
Warning: ListManager-methods.Rd:102: unknown macro '\item'
Warning: ListManager-methods.Rd:105: unknown macro '\item'
Warning: ListManager-methods.Rd:108: unknown macro '\item'
Warning: ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:117: unknown macro '\item'
Warning: ListManager-methods.Rd:120: unknown macro '\item'
Warning: ListManager-methods.Rd:123: unknown macro '\item'
Warning: ListManager-methods.Rd:126: unknown macro '\item'
Warning: ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:135: unknown macro '\item'
Warning: ListManager-methods.Rd:138: unknown macro '\item'
Warning: ListManager-methods.Rd:141: unknown macro '\item'
Warning: ListManager-methods.Rd:144: unknown macro '\item'
Warning: 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-3.18-bioc-mac-arm64/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
* 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 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: ListManager-methods.Rd:41: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:42: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:50: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:51: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:59: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:60: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:63: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:66: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:69: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:72: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:80: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:81: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:84: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:87: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:90: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:98: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:99: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:102: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:105: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:108: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:116: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:117: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:120: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:123: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:126: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:134: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:135: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:138: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:141: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:144: unknown macro '\item'
prepare_Rd: 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 ... 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 documentation object 'convertToGeneAnswers' but not in code:
‘convertToGeneAnswers’
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simplifyResult 7.426 0.298 9.297
* 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: 6 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/InterMineR.Rcheck/00check.log’
for details.
InterMineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL InterMineR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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: ListManager-methods.Rd:41: unexpected section header '\arguments' Warning: ListManager-methods.Rd:42: unknown macro '\item' Warning: ListManager-methods.Rd:50: unexpected section header '\arguments' Warning: ListManager-methods.Rd:51: unknown macro '\item' Warning: ListManager-methods.Rd:59: unexpected section header '\arguments' Warning: ListManager-methods.Rd:60: unknown macro '\item' Warning: ListManager-methods.Rd:63: unknown macro '\item' Warning: ListManager-methods.Rd:66: unknown macro '\item' Warning: ListManager-methods.Rd:69: unknown macro '\item' Warning: ListManager-methods.Rd:72: unknown macro '\item' Warning: ListManager-methods.Rd:80: unexpected section header '\arguments' Warning: ListManager-methods.Rd:81: unknown macro '\item' Warning: ListManager-methods.Rd:84: unknown macro '\item' Warning: ListManager-methods.Rd:87: unknown macro '\item' Warning: ListManager-methods.Rd:90: unknown macro '\item' Warning: ListManager-methods.Rd:98: unexpected section header '\arguments' Warning: ListManager-methods.Rd:99: unknown macro '\item' Warning: ListManager-methods.Rd:102: unknown macro '\item' Warning: ListManager-methods.Rd:105: unknown macro '\item' Warning: ListManager-methods.Rd:108: unknown macro '\item' Warning: ListManager-methods.Rd:116: unexpected section header '\arguments' Warning: ListManager-methods.Rd:117: unknown macro '\item' Warning: ListManager-methods.Rd:120: unknown macro '\item' Warning: ListManager-methods.Rd:123: unknown macro '\item' Warning: ListManager-methods.Rd:126: unknown macro '\item' Warning: ListManager-methods.Rd:134: unexpected section header '\arguments' Warning: ListManager-methods.Rd:135: unknown macro '\item' Warning: ListManager-methods.Rd:138: unknown macro '\item' Warning: ListManager-methods.Rd:141: unknown macro '\item' Warning: ListManager-methods.Rd:144: unknown macro '\item' Warning: 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’ ** 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’ ** testing if installed package keeps a record of temporary installation path * DONE (InterMineR)
InterMineR.Rcheck/InterMineR-Ex.timings
| name | user | system | elapsed | |
| InterMineR-methods | 0.082 | 0.019 | 0.734 | |
| ListManager-methods | 0.000 | 0.001 | 0.001 | |
| PL_DiabetesGenes | 0.002 | 0.001 | 0.004 | |
| PL_FlyTF_site_specific_TFs | 0.000 | 0.001 | 0.002 | |
| convertToGRanges | 0.564 | 0.027 | 1.534 | |
| convertToGeneAnswers | 0.001 | 0.001 | 0.000 | |
| convertToRangedSummarizedExperiment | 2.012 | 0.078 | 4.241 | |
| doEnrichment | 0.000 | 0.001 | 0.000 | |
| getDatasets | 0.092 | 0.006 | 1.226 | |
| getGeneIds | 0.360 | 0.015 | 1.994 | |
| getModel | 0.000 | 0.000 | 0.001 | |
| getRelease | 0.016 | 0.001 | 0.371 | |
| getTemplateQuery | 0.019 | 0.001 | 0.285 | |
| getTemplates | 0.028 | 0.002 | 0.334 | |
| getVersion | 0.018 | 0.001 | 0.287 | |
| getWidgets | 0.042 | 0.002 | 0.571 | |
| initInterMine | 0 | 0 | 0 | |
| listDatasets | 0 | 0 | 0 | |
| listMines | 0.009 | 0.001 | 0.251 | |
| list_manager | 0 | 0 | 0 | |
| newQuery | 0.000 | 0.001 | 0.001 | |
| runQuery | 1.922 | 0.022 | 4.422 | |
| setConstraints | 0.031 | 0.003 | 0.642 | |
| setQuery | 0.031 | 0.004 | 0.542 | |
| simplifyResult | 7.426 | 0.298 | 9.297 | |
| summary | 0.023 | 0.001 | 0.378 | |