===============================
R CMD BUILD
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* checking for file ‘scHiCcompare/DESCRIPTION’ ... OK
* preparing ‘scHiCcompare’:
* 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 ‘scHiCcompare_0.99.5.tar.gz’
===============================
BiocCheckGitClone('scHiCcompare')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3649/6091b7d763f154ea3292239664f08499e19cb99c/scHiCcompare
→ BiocVersion: 3.21
→ Package: scHiCcompare
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3649/6091b7d763f154ea3292239664f08499e19cb99c/scHiCcompare.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3649/6091b7d763f154ea3292239664f08499e19cb99c/scHiCcompare
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i 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 v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3649/6091b7d763f154ea3292239664f08499e19cb99c/scHiCcompare.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scHiCcompare/DESCRIPTION’ ... OK
* this is package ‘scHiCcompare’ version ‘0.99.5’
* 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 ‘scHiCcompare’ 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
inst/CITATION.txt
Most likely ‘inst/CITATION’ should be used instead.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [35s/35s] NOTE
.all_progressive_pooling: no visible global function definition for
‘tail’
.randomize_IFs: no visible global function definition for ‘rnorm’
GMM_layer: no visible global function definition for ‘shapiro.test’
RF_impute.outrm.schic: no visible global function definition for
‘boxplot.stats’
RF_impute.outrm.schic: no visible global function definition for
‘na.omit’
RF_impute.outrm.schic: no visible global function definition for
‘aggregate’
RF_impute.outrm.schic: no visible binding for global variable
‘Single_cell’
RF_impute.outrm.schic: no visible binding for global variable ‘IF’
RF_process: no visible global function definition for ‘boxplot.stats’
RF_process: no visible global function definition for ‘na.omit’
RF_process: no visible global function definition for ‘aggregate’
RF_process: no visible binding for global variable ‘Single_cell’
RF_process: no visible binding for global variable ‘IF’
best_A: no visible global function definition for ‘is’
best_A: no visible global function definition for ‘quantile’
differential_result_plot: no visible binding for global variable
‘adj.M’
differential_result_plot: no visible binding for global variable ‘D’
differential_result_plot: no visible binding for global variable
‘Difference.cluster’
find.collinear: no visible global function definition for ‘cor’
mice.rf_impute: no visible global function definition for ‘quantile’
mice.rf_impute: no visible global function definition for ‘IQR’
mice.rf_impute: no visible global function definition for ‘na.omit’
mice.rf_impute: no visible global function definition for ‘aggregate’
plot_HiCmatrix_heatmap: no visible global function definition for
‘colorRampPalette’
plot_imputed_distance_diagnostic: no visible binding for global
variable ‘IF’
plot_imputed_distance_diagnostic: no visible binding for global
variable ‘Group’
pools_impute : process_pool: no visible global function definition for
‘na.omit’
pools_impute : process_pool: no visible binding for global variable
‘Single_cell’
pools_impute : process_pool: no visible binding for global variable
‘IF’
print.checkNumbers: no visible global function definition for ‘na.omit’
read_files: no visible global function definition for ‘read.delim’
scHiC_bulk_compare: no visible global function definition for ‘bpparam’
scHiCcompare: no visible global function definition for ‘bpparam’
scHiCcompare: no visible binding for global variable ‘cell_id’
scHiCcompare: no visible binding for global variable ‘region1’
scHiCcompare: no visible binding for global variable ‘region2’
scHiCcompare: no visible binding for global variable ‘IF’
scHiCcompare : <anonymous>: no visible global function definition for
‘write.table’
scHiCcompare: no visible global function definition for ‘write.table’
scHiCcompare_impute: no visible global function definition for
‘boxplot’
scHiCcompare_impute: no visible binding for global variable
‘Single_cell’
scHiCcompare_impute: no visible binding for global variable ‘IF’
withoutNorm_hicTable: no visible global function definition for ‘:=’
withoutNorm_hicTable: no visible binding for global variable ‘A’
Undefined global functions or variables:
:= A D Difference.cluster Group IF IQR Single_cell adj.M aggregate
boxplot boxplot.stats bpparam cell_id colorRampPalette cor is na.omit
quantile read.delim region1 region2 rnorm shapiro.test tail
write.table
Consider adding
importFrom("grDevices", "boxplot.stats", "colorRampPalette")
importFrom("graphics", "boxplot")
importFrom("methods", "is")
importFrom("stats", "D", "IQR", "aggregate", "cor", "na.omit",
"quantile", "rnorm", "shapiro.test")
importFrom("utils", "read.delim", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scHiCcompare 7.398 0.691 8.008
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [16s/16s]
[17s/17s] 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 ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3649/6091b7d763f154ea3292239664f08499e19cb99c/scHiCcompare.Rcheck/00check.log’
for details.
===============================
BiocCheck('scHiCcompare_0.99.5.tar.gz')
===============================
── Installing scHiCcompare ─────────────────────────────────────────────────────
✔ Package installed successfully
── scHiCcompare session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBhZQOR/file11f6aec30e13a/scHiCcompare
→ BiocVersion: 3.21
→ Package: scHiCcompare
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3649/6091b7d763f154ea3292239664f08499e19cb99c/scHiCcompare.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpBhZQOR/file11f6aec30e13a/scHiCcompare
→ installDir: /tmp/RtmpBhZQOR/file11f6aef575028
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scHiCcompare ───────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.2.0 to 4.5.0.
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (7%).
* Checking for pinned package versions in DESCRIPTION...
* 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 scHiCcompare...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• scHiC_bulk_compare.R (line 28, column 19)
• ...
• ScHiCcompare.R (line 115, column 43)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/scHiC_bulk_compare.R (line 307, column 5)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/read_files.R (line 81, column 32)
• ...
• R/ScHiCcompare.R (line 377, column 11)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/PseudoBulk_sparse.R (line 42, column 10)
• ...
• R/ScHiCcompare.R (line 149, column 15)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressMessages() in R/scHiC_bulk_compare.R (line 57, column 16)
• suppressMessages() in R/scHiC_bulk_compare.R (line 64, column 18)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
• scHiCcompare() (R/ScHiCcompare.R): 232 lines
• ...
• RF_impute.outrm.schic() (R/scHiCcompare_impute.R): 84 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 385 lines (15%) are > 80 characters long.
First few lines:
• R/ODC.bandnorm_chr20_1.R#L1 #' scHi-C data from oligodendrocyte (ODC ...
• ...
• vignettes/ScHiCcompare.Rmd#L525 The diagnostic visualizations demonstrat ...
i NOTE: Consider multiples of 4 spaces for line indents; 825 lines (32%) are
not.
First few lines:
• R/plot_HiCmatrix_heatmap.R#L40 color ...
• ...
• vignettes/ScHiCcompare.Rmd#L520 imp_sc_data = imp_MG_table, D = 4 ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 10 NOTES
i See the scHiCcompare.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.