InterMine Team
| Snapshot Date: 2024-04-28 14:00:16 -0400 (Sun, 28 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/InterMineR |
| git_branch: devel |
| git_last_commit: 9ec7c85 |
| git_last_commit_date: 2024-02-02 09:49:25 -0400 (Fri, 02 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-04-29 11:40:57 -0400 (Mon, 29 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
| 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 1051/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
InterMine Team
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: InterMineR |
| Version: 1.25.1 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings InterMineR_1.25.1.tar.gz |
| StartedAt: 2024-04-29 07:15:59 -0000 (Mon, 29 Apr 2024) |
| EndedAt: 2024-04-29 07:21:26 -0000 (Mon, 29 Apr 2024) |
| EllapsedTime: 326.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: InterMineR.Rcheck |
| Warnings: 6 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings InterMineR_1.25.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* this is package ‘InterMineR’ version ‘1.25.1’
* 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: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
Warning: /home/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 ‘/home/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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simplifyResult 11.391 0.993 21.242
convertToRangedSummarizedExperiment 3.021 0.802 14.447
runQuery 3.073 0.414 14.074
getGeneIds 0.511 0.152 7.825
* 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: 6 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck/00check.log’
for details.
InterMineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL InterMineR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item' Warning: /home/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)
InterMineR.Rcheck/InterMineR-Ex.timings
| name | user | system | elapsed | |
| InterMineR-methods | 0.061 | 0.016 | 2.412 | |
| ListManager-methods | 0.001 | 0.000 | 0.000 | |
| PL_DiabetesGenes | 0.002 | 0.000 | 0.003 | |
| PL_FlyTF_site_specific_TFs | 0.001 | 0.000 | 0.001 | |
| convertToGRanges | 0.701 | 0.088 | 2.550 | |
| convertToGeneAnswers | 0 | 0 | 0 | |
| convertToRangedSummarizedExperiment | 3.021 | 0.802 | 14.447 | |
| doEnrichment | 0 | 0 | 0 | |
| getDatasets | 0.129 | 0.056 | 3.222 | |
| getGeneIds | 0.511 | 0.152 | 7.825 | |
| getModel | 0 | 0 | 0 | |
| getRelease | 0.023 | 0.000 | 0.913 | |
| getTemplateQuery | 0.023 | 0.000 | 0.931 | |
| getTemplates | 0.035 | 0.000 | 1.470 | |
| getVersion | 0.023 | 0.000 | 0.911 | |
| getWidgets | 0.053 | 0.000 | 1.830 | |
| initInterMine | 0 | 0 | 0 | |
| listDatasets | 0 | 0 | 0 | |
| listMines | 0.012 | 0.000 | 0.628 | |
| list_manager | 0.000 | 0.000 | 0.001 | |
| newQuery | 0 | 0 | 0 | |
| runQuery | 3.073 | 0.414 | 14.074 | |
| setConstraints | 0.033 | 0.004 | 1.544 | |
| setQuery | 0.036 | 0.005 | 1.081 | |
| simplifyResult | 11.391 | 0.993 | 21.242 | |
| summary | 0.027 | 0.004 | 0.926 | |