===============================
R CMD BUILD
===============================
* checking for file ‘MIRit/DESCRIPTION’ ... OK
* preparing ‘MIRit’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘MIRit_0.99.2.tar.gz’
===============================
BiocCheckGitClone('MIRit')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: MIRit
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3249/1b94c1b4fc6c96624212c82af51effd752eb1f7b/MIRit
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3249/1b94c1b4fc6c96624212c82af51effd752eb1f7b/MIRit.Rcheck’
* using R Under development (unstable) (2023-11-11 r85510)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MIRit/DESCRIPTION’ ... OK
* this is package ‘MIRit’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MIRit’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'graphite:::convertEdges' 'graphite:::selectDb'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [31s/31s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [68s/68s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addDifferentialExpression 20.376 0.484 20.861
deAnalysis 5.033 0.068 5.101
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [68s/69s]
[69s/69s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
As specified by the user, a fry will be used.
Performing miRNA-gene integrative analysis using 'fry' method...
A statistically significant association between 17 DE-miRNAs and 77 genes was found!
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 57 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-targets.R:29:5'): miRTarBase is responsive ─────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [mirtarbase.cuhk.edu.cn] Operation timed out after 4001 milliseconds with 0 bytes received
Backtrace:
▆
1. └─httr::HEAD(mtUrl, httr::timeout(4)) at test-targets.R:29:5
2. └─httr:::request_perform(req, hu$handle$handle)
3. ├─httr:::request_fetch(req$output, req$url, handle)
4. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
5. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 57 ]
Error: Test failures
Execution halted
* 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 ... [4s/4s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3249/1b94c1b4fc6c96624212c82af51effd752eb1f7b/MIRit.Rcheck/00check.log’
for details.
===============================
BiocCheck('MIRit_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: MIRit
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpXMA8gn/file154cab98a890/MIRit
─ installDir: /tmp/RtmpXMA8gn/file154cab4efe29ca
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3249/1b94c1b4fc6c96624212c82af51effd752eb1f7b/MIRit.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MIRit...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 45 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 17% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* NOTE: skip_on_bioc() found in testthat files: test-association.R
test-targets.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 466 lines (3%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 256 lines
(2%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 10 NOTES
See the MIRit.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.