===============================
BiocCheckGitClone('MGnifyR')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: MGnifyR
─ PackageVersion: 0.99.8
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3191/d3b090f77923c7d6202438ccc87d4c306a6d2061/MGnifyR
─ 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...
─ 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/3191/d3b090f77923c7d6202438ccc87d4c306a6d2061/MGnifyR.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 ‘MGnifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MGnifyR’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'mia', 'MultiAssayExperiment', 'TreeSummarizedExperiment',
'SummarizedExperiment', 'biomformat', 'BiocGenerics'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘MGnifyR’ can be installed ... OK
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘BiocGenerics’ ‘biomformat’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘BiocGenerics:::replaceSlots’
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 ... [34s/34s] OK
* checking Rd files ... [0s/0s] 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 files in ‘vignettes’ ... OK
* checking examples ... [15s/31s] ERROR
Running examples in ‘MGnifyR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getFile
> ### Title: Download any MGnify files, also including processed reads and
> ### identified protein sequences
> ### Aliases: getFile searchFile getFile,MgnifyClient-method
> ### searchFile,MgnifyClient-method
>
> ### ** Examples
>
> # Make a client object
> mg <- MgnifyClient(useCache = FALSE)
>
> # Create a vector of accession ids - these happen to be \code{analysis}
> # accessions
> accession_vect <- c("MGYA00563876", "MGYA00563877")
> downloads <- searchFile(mg, accession_vect, "analyses")
Searching files...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
>
> # Filter to find the urls of 16S encoding sequences
> url_list <- downloads[
+ downloads$attributes.description.label == "Contigs encoding SSU rRNA",
+ "download_url"]
>
> # Example 1:
> # Download the first file
> supplied_filename <- getFile(
+ mg, url_list[[1]], file="SSU_file.fasta.gz")
>
>
> # Make a client object
> mg <- MgnifyClient(useCache = TRUE)
> # Create a vector of accession ids - these happen to be \code{analysis}
> # accessions
> accession_vect <- c(
+ "MGYA00563876", "MGYA00563877", "MGYA00563878",
+ "MGYA00563879", "MGYA00563880" )
> downloads <- searchFile(mg, accession_vect, "analyses")
Searching files...
|
| | 0%
|
|============== | 20%
|
|============================ | 40%Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [www.ebi.ac.uk] Operation timed out after 10001 milliseconds with 0 bytes received
Calls: searchFile ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/170s]
[13s/170s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.ebi.ac.uk] Operation timed out after 10001 milliseconds with 0 bytes received
Backtrace:
▆
1. ├─MGnifyR::getResult(mg, "MGYA00097621", get.func = TRUE, verbose = FALSE) at test-getResult.R:48:5
2. └─MGnifyR::getResult(mg, "MGYA00097621", get.func = TRUE, verbose = FALSE)
3. └─MGnifyR (local) .local(x, ...)
4. └─MGnifyR:::.mgnify_get_analyses_results(...)
5. └─plyr::llply(...)
6. ├─plyr:::loop_apply(n, do.ply)
7. └─plyr (local) `<fn>`(1L)
8. └─MGnifyR (local) .fun(piece, ...)
9. └─MGnifyR:::.mgnify_get_single_analysis_results(...)
10. └─MGnifyR:::.mgnify_retrieve_json(...)
11. └─httr::GET(...)
12. └─httr:::request_perform(req, hu$handle$handle)
13. ├─httr:::request_fetch(req$output, req$url, handle)
14. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
15. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 144 ]
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 ... [3s/3s] OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3191/d3b090f77923c7d6202438ccc87d4c306a6d2061/MGnifyR.Rcheck/00check.log’
for details.
===============================
BiocCheck('MGnifyR_0.99.8.tar.gz')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: MGnifyR
─ PackageVersion: 0.99.8
─ sourceDir: /tmp/Rtmps6pLtz/file27041e101e1410/MGnifyR
─ installDir: /tmp/Rtmps6pLtz/file27041e8c88df1
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3191/d3b090f77923c7d6202438ccc87d4c306a6d2061/MGnifyR.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 4.3 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* 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 MGnifyR...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 14 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 56% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 9 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 106 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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 1 WARNINGS | 8 NOTES
See the MGnifyR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.