===============================
R CMD BUILD
===============================
* checking for file ‘hdxmsqc/DESCRIPTION’ ... OK
* preparing ‘hdxmsqc’:
* 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 ‘hdxmsqc_0.99.3.tar.gz’
===============================
BiocCheckGitClone('hdxmsqc')
===============================
─ BiocCheckVersion: 1.39.27
─ BiocVersion: 3.19
─ Package: hdxmsqc
─ PackageVersion: 0.99.3
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3311/cfddc4754bdb6d90bb597d78ee267451bd8222ab/hdxmsqc
─ 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...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3311/cfddc4754bdb6d90bb597d78ee267451bd8222ab/hdxmsqc.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hdxmsqc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hdxmsqc’ version ‘0.99.3’
* 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 ‘hdxmsqc’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [31s/31s] NOTE
chargeCorrelationHdx: no visible global function definition for ‘assay’
chargeCorrelationHdx: no visible binding for global variable ‘x’
chargeCorrelationHdx: no visible binding for global variable ‘z’
chargeCorrelationHdx: no visible binding for global variable ‘peptide’
chargeCorrelationHdx: no visible binding for global variable ‘y’
compatibleUptake: no visible global function definition for ‘rowData’
compatibleUptake: no visible global function definition for ‘assay’
computeMassError: no visible global function definition for ‘rowData’
computeMassError: no visible global function definition for ‘assay’
computeMonotoneStats: no visible global function definition for ‘assay’
computeMonotoneStats: no visible binding for global variable ‘x’
computeMonotoneStats: no visible binding for global variable ‘y’
imTimeOutlier: no visible global function definition for ‘rowData’
imTimeOutlier: no visible global function definition for ‘rowMedians’
imTimeOutlier: no visible binding for global variable ‘Experiment’
imTimeOutlier: no visible binding for global variable ‘IMS_shift’
intensityOutliers: no visible global function definition for ‘rowData’
isMissingAtRandom: no visible global function definition for ‘assay’
isMissingAtRandom: no visible global function definition for ‘rowData’
plotImTimeOutlier: no visible binding for global variable ‘Experiment’
plotImTimeOutlier: no visible binding for global variable ‘IMS_shift’
plotImTimeOutlier: no visible global function definition for
‘brewer.pal’
plotIntensityOutliers: no visible binding for global variable ‘x’
plotIntensityOutliers: no visible binding for global variable ‘y’
plotIntensityOutliers: no visible binding for global variable ‘outlier’
plotIntensityOutliers: no visible global function definition for
‘brewer.pal’
plotMassError: no visible binding for global variable ‘x’
plotMassError: no visible binding for global variable ‘y’
plotMassError: no visible global function definition for ‘brewer.pal’
plotMissing: no visible global function definition for ‘assay’
plotMissing: no visible global function definition for ‘pheatmap’
plotMissing: no visible global function definition for ‘brewer.pal’
plotMonotoneStat : <anonymous>: no visible binding for global variable
‘x’
plotMonotoneStat : <anonymous>: no visible binding for global variable
‘y’
plotMonotoneStat : <anonymous>: no visible binding for global variable
‘outlier’
plotMonotoneStat : <anonymous>: no visible global function definition
for ‘brewer.pal’
plotrTimeOutliers: no visible binding for global variable ‘Experiment’
plotrTimeOutliers: no visible binding for global variable ‘RT_shift’
plotrTimeOutliers: no visible global function definition for
‘brewer.pal’
processHDE: no visible binding for global variable ‘Deut.Time’
processHDE: no visible binding for global variable ‘Sequence’
processHDE: no visible binding for global variable ‘Protein.State’
processHDE: no visible binding for global variable ‘Charge’
qualityControl: no visible global function definition for ‘rowData’
rTimeOutliers: no visible global function definition for ‘rowData’
rTimeOutliers: no visible global function definition for ‘rowMedians’
rTimeOutliers: no visible binding for global variable ‘Experiment’
rTimeOutliers: no visible binding for global variable ‘RT_shift’
replicateCorrelation: no visible global function definition for ‘assay’
replicateCorrelation: no visible binding for global variable ‘x’
replicateCorrelation: no visible binding for global variable ‘y’
replicateOutlier: no visible global function definition for ‘assay’
replicateOutlier: no visible binding for global variable ‘x’
replicateOutlier: no visible binding for global variable ‘y’
spectraSimilarity: no visible global function definition for ‘bpparam’
spectraSimilarity: no visible binding for global variable ‘timepoints’
spectraSimilarity: no visible binding for global variable ‘Sequence’
spectraSimilarity: no visible global function definition for ‘bplapply’
spectraSimilarity: no visible global function definition for
‘spectraData’
spectraSimilarity: no visible binding for global variable ‘Charge’
spectraSimilarity: no visible binding for global variable ‘DeutTime’
Undefined global functions or variables:
Charge Deut.Time DeutTime Experiment IMS_shift Protein.State RT_shift
Sequence assay bplapply bpparam brewer.pal outlier peptide pheatmap
rowData rowMedians spectraData timepoints x y z
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'processHDE.Rd':
\examples lines wider than 100 characters:
sample_data <- data.frame(read.csv(system.file("extdata", "ELN55049_AllResultsTables_Uncurated.csv", package = "hdxmsqc", mustWork = TR ... [TRUNCATED]
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 ... [15s/17s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [58s/58s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotMonotoneStat 5.738 0.08 5.819
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [15s/15s]
[15s/15s] OK
* 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 ... [4s/4s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3311/cfddc4754bdb6d90bb597d78ee267451bd8222ab/hdxmsqc.Rcheck/00check.log’
for details.
===============================
BiocCheck('hdxmsqc_0.99.3.tar.gz')
===============================
─ BiocCheckVersion: 1.39.27
─ BiocVersion: 3.19
─ Package: hdxmsqc
─ PackageVersion: 0.99.3
─ sourceDir: /tmp/Rtmp2zJ0mj/file41531669f2474/hdxmsqc
─ installDir: /tmp/Rtmp2zJ0mj/file415314531c368
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3311/cfddc4754bdb6d90bb597d78ee267451bd8222ab/hdxmsqc.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...
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 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (38%).
* 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 hdxmsqc...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 6 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.
* 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; 103 lines (5%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 219 lines
(11%) 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 is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 8 NOTES
See the hdxmsqc.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.