===============================
R CMD BUILD
===============================
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* preparing ‘iNETgrate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* 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 ‘iNETgrate_0.99.17.tar.gz’
===============================
BiocCheckGitClone('iNETgrate')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: iNETgrate
─ PackageVersion: 0.99.17
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2979/62282ee76487ae59a10f0533cf5f40bae4da48c1/iNETgrate
─ 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/2979/62282ee76487ae59a10f0533cf5f40bae4da48c1/iNETgrate.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iNETgrate’ version ‘0.99.17’
* 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 ‘iNETgrate’ 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 ... [16s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the namespace can be unloaded cleanly ... [16s/16s] OK
* checking loading without being on the library search path ... [16s/16s] OK
* checking use of S3 registration ... 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 ... [51s/51s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'survival.analysis.Rd':
\examples lines wider than 100 characters:
Pigengene::pheatmap.type(Data=scale(toPlot), annRow=as.data.frame(patientLabel[rownames(toPlot)]), cluster_cols=FALSE)
These lines will be truncated in the PDF manual.
* 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 ... [5s/5s] OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
toyCleanedAml.rda 1.9Mb 1.7Mb xz
toyComputEloci.rda 124Kb 105Kb xz
toyRawAml.rda 2.1Mb 1.8Mb xz
* checking files in ‘vignettes’ ... OK
* checking examples ... [117s/145s] ERROR
Running examples in ‘iNETgrate-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download.data
> ### Title: Download and save TCGA data
> ### Aliases: download.data
> ### Keywords: data
>
> ### ** Examples
>
> tcgaAml <- download.data(dataProject="TCGA-LAML", savePath=getwd(),
+ doDnam=FALSE, doClinical=TRUE,
+ doExpr=FALSE, doMirna = FALSE, legacy=TRUE)
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-LAML
--------------------
oo Filtering results
--------------------
ooo By file.type
----------------
oo Checking data
----------------
ooo Checking if there are duplicated cases
ooo Checking if there are results for the query
-------------------
o Preparing output
-------------------
Downloading data for project TCGA-LAML
GDCdownload will download 200 files. A total of 9.238562 MB
Downloading as: Mon_Apr__3_09_40_27_2023.tar.gz
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To get the following information please change the clinical.info argument
=> new_tumor_events: new_tumor_event
=> drugs: drug
=> follow_ups: follow_up
=> radiations: radiation
Updating days_to_last_followup and vital_status from follow_up information using last entry
Error in `dplyr::group_by()`:
! Must group by variables found in `.data`.
✖ Column `bcr_patient_barcode` is not found.
Backtrace:
▆
1. ├─iNETgrate::download.data(...)
2. │ └─TCGAbiolinks::GDCprepare_clinic(...)
3. │ └─followup %>% dplyr::group_by(bcr_patient_barcode) %>% ...
4. ├─dplyr::summarise(...)
5. ├─dplyr::group_by(., bcr_patient_barcode)
6. └─dplyr:::group_by.data.frame(., bcr_patient_barcode)
7. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env())
8. └─rlang::abort(bullets, call = error_call)
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: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2979/62282ee76487ae59a10f0533cf5f40bae4da48c1/iNETgrate.Rcheck/00check.log’
for details.
===============================
BiocCheck('iNETgrate_0.99.17.tar.gz')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: iNETgrate
─ PackageVersion: 0.99.17
─ sourceDir: /tmp/Rtmpsnqjzl/file69c4673ebafb0/iNETgrate
─ installDir: /tmp/Rtmpsnqjzl/file69c46711af102
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2979/62282ee76487ae59a10f0533cf5f40bae4da48c1/iNETgrate.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 3.5.0 to 4.3.0.
* 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...
* 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 iNETgrate...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* WARNING: Remove browser() statements (found 2 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 23 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
Registered S3 method overwritten by 'gplots':
method from
reorder.factor gdata
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 6% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 700 lines (11%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1040 lines
(16%) 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 | 2 WARNINGS | 9 NOTES
See the iNETgrate.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.