===============================
R CMD BUILD
===============================
* checking for file ‘rawDiag/DESCRIPTION’ ... OK
* preparing ‘rawDiag’:
* 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
* building ‘rawDiag_0.99.14.tar.gz’
===============================
BiocCheckGitClone('rawDiag')
===============================
─ BiocCheckVersion: 1.39.18
─ BiocVersion: 3.19
─ Package: rawDiag
─ PackageVersion: 0.99.14
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3251/8f6f36fb620a80cbbc2e2da31c37184eb4cf4bf4/rawDiag
─ 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/3251/8f6f36fb620a80cbbc2e2da31c37184eb4cf4bf4/rawDiag.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 ‘rawDiag/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rawDiag’ version ‘0.99.14’
* 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 ‘rawDiag’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.read.raw’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] 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 ... [1s/1s] ERROR
Running examples in ‘rawDiag-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .fillNAgaps
> ### Title: Fill NA values with last previous value
> ### Aliases: .fillNAgaps
>
> ### ** Examples
>
> c(NA, 1, 2, 3, NA, 4, 5, NA, NA, NA, 6) |>
+ .fillNAgaps()
Error in .fillNAgaps(c(NA, 1, 2, 3, NA, 4, 5, NA, NA, NA, 6)) :
could not find function ".fillNAgaps"
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [5s/4s]
[5s/5s] OK
* 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 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3251/8f6f36fb620a80cbbc2e2da31c37184eb4cf4bf4/rawDiag.Rcheck/00check.log’
for details.
===============================
BiocCheck('rawDiag_0.99.14.tar.gz')
===============================
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3251/8f6f36fb620a80cbbc2e2da31c37184eb4cf4bf4/rawDiag_0.99.14.tar.gz
must be loadable.
─ BiocCheckVersion: 1.39.18
─ BiocVersion: 3.19
─ Package: rawDiag
─ PackageVersion: 0.99.14
─ sourceDir: /tmp/RtmpxIm7WZ/file3c4f9f31e1725b/rawDiag
─ installDir: /tmp/RtmpxIm7WZ/file3c4f9f5eeb8427
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3251/8f6f36fb620a80cbbc2e2da31c37184eb4cf4bf4/rawDiag.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...
* 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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (8%).
* Checking for pinned package versions in DESCRIPTION...
* 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 rawDiag...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 5 functions greater than 50 lines.
* Checking man page documentation...
Error in namespaceExport(ns, exports) :
undefined exports: PlotChargeState, PlotCycleTime, PlotInjectionTime, PlotLockMassCorrection, PlotMassDistribution, PlotMzDistribution, PlotPrecursorHeatmap, PlotScanTime, PlotTicBasepeak
Calls: BiocCheck ... checkExportsAreDocumented -> loadNamespace -> namespaceExport
Execution halted