===============================
BiocCheckGitClone('BCalm')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3684/BCalm_20250113180006/BCalm
BiocVersion: 3.21
Package: BCalm
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3684/BCalm_20250113180006/BCalm.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3684/BCalm_20250113180006/BCalm
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3684/BCalm_20250113180006/BCalm/.gitignore'
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.43.2 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3684/BCalm_20250113180006/BCalm.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 BCalm/DESCRIPTION ... OK
* this is package BCalm version 0.99.0
* 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 BCalm can be installed ... WARNING
Found the following significant warnings:
Warning: changing locked binding for compute_logratio in mpra whilst loading BCalm
See /home/pkgbuild/packagebuilder/workers/jobs/3684/BCalm_20250113180006/BCalm.Rcheck/00install.out for details.
* 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 components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] WARNING
Error: .onLoad failed in loadNamespace() for 'BCalm', details:
call: assignInNamespace("compute_logratio", compute_logratio, ns = "mpra")
error: could not find function "assignInNamespace"
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking whether startup messages can be suppressed ... [6s/6s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: .onLoad failed in loadNamespace() for 'BCalm', details:
call: assignInNamespace("compute_logratio", compute_logratio, ns = "mpra")
error: could not find function "assignInNamespace"
Call sequence:
3: stop(gettextf("%s failed in %s() for '%s', details:\n call: %s\n error: %s",
hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L],
conditionMessage(res)), call. = FALSE, domain = NA)
2: runHook(".onLoad", env, package.lib, package)
1: loadNamespace(package, lib.loc)
Execution halted
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [19s/19s] NOTE
Found the following possibly unsafe calls:
File BCalm/R/utils.R:
assignInNamespace("compute_logratio", compute_logratio, ns = "mpra")
Error: .onLoad failed in loadNamespace() for 'BCalm', details:
call: assignInNamespace("compute_logratio", compute_logratio, ns = "mpra")
error: could not find function "assignInNamespace"
Execution halted
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) BCalm-package.Rd:36: Lost braces
36 | Smyth, Gordon K., Jo\"{e}lle Michaud, and Hamish S. Scott.
| ^
checkRd: (-1) mpralm.Rd:55: Lost braces
55 | Smyth, Gordon K., Jo\"{e}lle Michaud, and Hamish S. Scott.
| ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
BcSetExample LabelExample MapExample MapExampleOriginalIds
create_dna_df create_rna_df create_var_df downsample_barcodes
fit_elements getLabel mpra_treat plot_groups
Undocumented data sets:
BcSetExample LabelExample MapExample MapExampleOriginalIds
All user-level objects in a package should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking for code/documentation mismatches ... WARNING
Data with usage in Rd file 'mpraSetExample.Rd' but not in code:
mpraSetExample mpraSetAggExample mpraSetAllelicExample
Codoc mismatches from Rd file 'MPRASet-class.Rd':
MPRASet
Code: function(label = new("character"), ...)
Docs: function(DNA = new("matrix"), RNA = new("matrix"), barcode =
new("character"), eid = new("character"), eseq =
new("character"), ...)
Argument names in code not in docs:
label
Argument names in docs not in code:
DNA RNA barcode eid eseq
Mismatches in argument names:
Position: 1 Code: label Docs: DNA
Position: 2 Code: ... Docs: RNA
Codoc mismatches from Rd file 'mpralm.Rd':
mpralm
Code: function(object, design, aggregate = c("mean", "sum", "none"),
normalize = TRUE, normalizeSize = 1e+07, block = NULL,
model_type = c("indep_groups", "corr_groups"), plot =
TRUE, endomorphic = FALSE, ...)
Docs: function(object, design, aggregate = c("mean", "sum", "none"),
normalize = TRUE, block = NULL, model_type =
c("indep_groups", "corr_groups"), plot = TRUE, ...)
Argument names in code not in docs:
normalizeSize endomorphic
Mismatches in argument names (first 3):
Position: 5 Code: normalizeSize Docs: block
Position: 6 Code: block Docs: model_type
Position: 7 Code: model_type Docs: plot
Codoc mismatches from Rd file 'normalize_counts.Rd':
normalize_counts
Code: function(object, normalizeSize = 1e+07, block = NULL)
Docs: function(object, block = NULL)
Argument names in code not in docs:
normalizeSize
Mismatches in argument names:
Position: 2 Code: normalizeSize Docs: block
* 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 ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [7s/7s] ERROR
Running examples in BCalm-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BCalm-package
> ### Title: Barcode Analysis using linear models
> ### Aliases: BCalm-package BCalm
> ### Keywords: package
>
> ### ** Examples
>
> data(mpraSetAggExample)
Warning in data(mpraSetAggExample) :
data set mpraSetAggExample not found
> design <- data.frame(intcpt = 1,
+ episomal = grepl("MT", colnames(mpraSetAggExample)))
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'grepl': error in evaluating the argument 'x' in selecting a method for function 'colnames': object 'mpraSetAggExample' not found
Calls: data.frame ... colnames -> .handleSimpleError -> h -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in tests ... WARNING
'library' or 'require' calls not declared from:
devtools dplyr here usethis
* checking tests ...
Running runTests.R [0s/0s]
Running testthat.R [6s/6s]
[7s/7s] ERROR
Running the tests in tests/runTests.R failed.
Complete output:
> library(testthat)
> library(usethis)
Error in library(usethis) : there is no package called 'usethis'
Execution halted
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
1. mpra::MPRASet(...) at test-analyze.R:18:1
2. methods::new(...)
3. methods::initialize(value, ...)
4. methods::initialize(value, ...)
Error ('test-fit.R:15:1'): (code run outside of `test_that()`)
Error in `SummarizedExperiment(assays = assays, rowData = rowData, ...)`: unused argument (label = c("test_label_1", "test_label_1", "test_label_1", "test_label_1", "test_label_1", "test_label_2", "test_label_2", "test_label_2", "test_label_2", "test_label_2"))
Backtrace:
1. mpra::MPRASet(...) at test-fit.R:15:1
2. methods::new(...)
3. methods::initialize(value, ...)
4. methods::initialize(value, ...)
Error ('test-preprocess.R:3:1'): (code run outside of `test_that()`)
<packageNotFoundError/error/condition>
Error in `library(usethis)`: there is no package called 'usethis'
Backtrace:
1. base::library(usethis) at test-preprocess.R:3:1
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
* 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: 2 ERRORs, 5 WARNINGs, 5 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3684/BCalm_20250113180006/BCalm.Rcheck/00check.log
for details.
===============================
BiocCheck('BCalm_0.99.0.tar.gz')
===============================
Installing BCalm
Package installed successfully
BCalm session metadata
sourceDir: /tmp/RtmpykQcOJ/file13295684ed780/BCalm
BiocVersion: 3.21
Package: BCalm
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3684/BCalm_20250113180006/BCalm.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpykQcOJ/file13295684ed780/BCalm
installDir: /tmp/RtmpykQcOJ/file1329563f37b0a
isTarBall: TRUE
platform: unix
Running BiocCheck on BCalm
* 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 3.5 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...
i NOTE: Consider adding these automatically suggested biocViews: Microarray,
Coverage, DifferentialExpression, KEGG, Preprocessing, Regression
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (59%).
* 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 BCalm...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/analyze.R (line 24, column 17)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/preprocess.R (line 3, column 25)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
suppressWarnings() in R/preprocess.R (line 44, column 9)
suppressWarnings() in R/preprocess.R (line 54, column 9)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
The longest 5 functions are:
mpra_treat() (R/analyze.R): 69 lines
plot_groups() (R/analyze.R): 54 lines
* Checking man page documentation...
Warning: changing locked binding for compute_logratio in mpra whilst loading BCalm
* 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; 78 lines (9%) are > 80 characters long.
First few lines:
R/analyze.R#L1 plot_groups <- function(object, percenti ...
...
vignettes/BCalm.Rmd#L165 The `mpra_treat()` function reimplements ...
i NOTE: Consider 4 spaces instead of tabs; 221 lines (25%) contain tabs.
First few lines:
R/analyze.R#L2 if (is(object, "MPRASet")) { ...
...
R/preprocess.R#L116 return(df_pivot) ...
i NOTE: Consider multiples of 4 spaces for line indents; 116 lines (13%) are
not.
First few lines:
R/utils.R#L7 # Override the compute_logratio functi ...
...
vignettes/BCalm.Rmd#L143 geom_point(alpha = 0.6) ...
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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
BiocCheck v1.43.2 results
2 ERRORS | 0 WARNINGS | i 11 NOTES
i See the BCalm.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.