===============================
BiocCheckGitClone('octad')
===============================
This is BiocCheckGitClone version 1.30.0. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
octad.Rproj
R/.Rapp.history
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
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R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2391/b1f80f983c4e7eaa8a3019ac6bd44cba31a3e040/octad.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad/DESCRIPTION’ ... OK
* this is package ‘octad’ version ‘0.99.14’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependency missing from DESCRIPTION Imports/Depends entries: ‘ExperimentHub’
Depends: includes the non-default packages:
'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma',
'rhdf5', 'doParallel', 'foreach', 'Rfast', 'octad.db', 'httr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2391/b1f80f983c4e7eaa8a3019ac6bd44cba31a3e040/octad.Rcheck/00check.log’
for details.
===============================
BiocCheck('octad_0.99.14.tar.gz')
===============================
This is BiocCheck version 1.30.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 43 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
computeCellLine (cell.line)
computeCellLine (write.csv)
computeRefTissue (sample.type)
computeRefTissue (.)
computeRefTissue (sample.id)
computeRefTissue (write.csv)
diffExp (pData)
diffExp (write.csv)
diffExp (identifier)
diffExp (case)
diffExp (control)
geneEnrich (write.csv)
octadDrugEnrichment (mcols)
octadDrugEnrichment (query)
octadDrugEnrichment (title)
octadDrugEnrichment (write.csv)
octadDrugEnrichment (pdf)
octadDrugEnrichment (dev.off)
octadDrugEnrichment (read.csv2)
plot_bsabs (pair_score)
plot_bsabs (p.adj)
plot_bsabs (significant)
plot_bsabs (pair_label)
runsRGES (cell_id)
runsRGES (pert_iname)
runsRGES (pert_id)
runsRGES (write.csv)
runsRGES (Symbol)
runsRGES (log2FoldChange)
runsRGES (head)
runsRGES (txtProgressBar)
runsRGES (read.csv)
runsRGES (pert_dose)
runsRGES (pert_time)
runsRGES (id.x)
runsRGES (id.y)
runsRGES (pert_time.x)
runsRGES (pert_dose.x)
runsRGES (RGES)
topLineEval (sRGES)
topLineEval (medIC50)
topLineEval (pert_iname)
topLineEval (medauc)
* 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 4.0 to 4.1.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, Epigenetics, Transcriptomics,
Coverage, GeneSetEnrichment, Normalization, Pathways,
Preprocessing, Bayesian, Clustering, Regression, DNAMethylation,
RNASeq, ChIPSeq, CellBiology, BiomedicalInformatics,
FunctionalGenomics, SystemsBiology, ImmunoOncology,
AlternativeSplicing, DifferentialExpression,
DifferentialMethylation, DifferentialSplicing, BatchEffect,
MultipleComparison, QualityControl, TimeCourse
See http://bioconductor.org/developers/how-to/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 DESCRIPTION/NAMESPACE consistency...
* WARNING: Import ExperimentHub in DESCRIPTION as well as
NAMESPACE.
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of octad...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/octadDrugEnrichment.R (line 88, column 13)
R/runsRGES_ultimate.R (line 51, column 29)
R/runsRGES_ultimate.R (line 54, column 29)
R/runsRGES_ultimate.R (line 70, column 31)
R/runsRGES_ultimate.R (line 73, column 31)
R/runsRGES_ultimate.R (line 260, column 14)
R/runsRGES_ultimate.R (line 298, column 22)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
computeCellLine.R (line 42, column 60)
computeCellLine.R (line 95, column 76)
computeRefTissue.R (line 75, column 58)
diffExp.R (line 39, column 60)
diffExp.R (line 43, column 62)
diffExp.R (line 117, column 54)
geneEnrich.R (line 28, column 19)
loadOctadCounts.R (line 14, column 65)
loadOctadCounts.R (line 24, column 63)
plot_bsabs.R (line 23, column 93)
plot_bsabs.R (line 26, column 96)
plot_bsabs.R (line 29, column 79)
runsRGES_ultimate.R (line 256, column 61)
runsRGES_ultimate.R (line 257, column 61)
runsRGES_ultimate.R (line 298, column 29)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths..................
* NOTE: Recommended function length <= 50 lines.
There are 7 functions > 50 lines.
The longest 5 functions are:
runsRGES() (R/runsRGES_ultimate.R, line 10): 315 lines
diffExp() (R/diffExp.R, line 8): 232 lines
topLineEval() (R/topLineEval.R, line 10): 171 lines
computeRefTissue() (R/computeRefTissue.R, line 7): 121 lines
computeCellLine() (R/computeCellLine.R, line 7): 119 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 305 lines (17%) are > 80 characters
long.
First 6 lines:
R/computeCellLine.R:7 computeCellLine <- function(case_id =case_id,expS...
R/computeCellLine.R:17 pick.out.cell.line <- function(expr.of.sampl...
R/computeCellLine.R:18 marker.gene <- inter...
R/computeCellLine.R:19 marker.gene <- inter...
R/computeCellLine.R:20 correlation.matrix <- cor(expr.of...
R/computeCellLine.R:22 cell.line.median.cor <- apply(correla...
* NOTE: Consider 4 spaces instead of tabs; 50 lines (3%) contain
tabs.
First 6 lines:
R/computeCellLine.R:59
R/computeCellLine.R:61
R/computeCellLine.R:62 octad.LINCS.counts=ExperimentHub()[["EH7273"]]
R/computeCellLine.R:64
R/computeCellLine.R:65 print(paste('computing correlation between cell...
R/computeCellLine.R:74
* NOTE: Consider multiples of 4 spaces for line indents, 134
lines(7%) are not.
First 6 lines:
R/computeCellLine.R:16 #helper function by Ke
R/computeRefTissue.R:8 adjacent=FALSE,
R/computeRefTissue.R:9 source='octad',n_va...
R/computeRefTissue.R:10 method='varGenes',...
R/computeRefTissue.R:11 expSet=NULL,
R/computeRefTissue.R:12 #site_selection = ...
See http://bioconductor.org/developers/how-to/coding-style/
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.
Summary:
ERROR count: 0
WARNING count: 1
NOTE count: 10
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output