===============================
BiocCheckGitClone('muSpaData')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3682/muSpaData_20250102162136/muSpaData
→ BiocVersion: 3.21
→ Package: muSpaData
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3682/muSpaData_20250102162136/muSpaData.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3682/muSpaData_20250102162136/muSpaData
→ 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...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
* 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 ───────────────────────────────────────────────────
✖ 1 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/3682/muSpaData_20250102162136/muSpaData.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 ‘muSpaData/DESCRIPTION’ ... OK
* this is package ‘muSpaData’ version ‘0.99.0’
* 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 ‘muSpaData’ 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 ... 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 ... [0s/0s] WARNING
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: read.csv(fn, stringsAsFactors = FALSE)
error: could not find function "read.csv"
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 ... [0s/0s] WARNING
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: createHubAccessors(pkgname, ts)
error: could not find function "createHubAccessors"
Execution halted
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: read.csv(fn, stringsAsFactors = FALSE)
error: could not find function "read.csv"
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 ... WARNING
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: createHubAccessors(pkgname, ts)
error: could not find function "createHubAccessors"
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
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: createHubAccessors(pkgname, ts)
error: could not find function "createHubAccessors"
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
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: createHubAccessors(pkgname, ts)
error: could not find function "createHubAccessors"
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
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [1s/1s] NOTE
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: createHubAccessors(pkgname, ts)
error: could not find function "createHubAccessors"
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
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: read.csv(fn, stringsAsFactors = FALSE)
error: could not find function "read.csv"
Execution halted
* 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 ... WARNING
Undocumented code objects:
‘Wei22_example’
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
Codoc mismatches from Rd file 'Wei22_full.Rd':
Wei22_full
Code: function(metadata = FALSE)
Docs: function()
Argument names in code not in docs:
metadata
* checking Rd \usage sections ... NOTE
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: createHubAccessors(pkgname, ts)
error: could not find function "createHubAccessors"
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
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/38s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Wei22_full 23.333 3.785 27.416
* 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: 6 WARNINGs, 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3682/muSpaData_20250102162136/muSpaData.Rcheck/00check.log’
for details.
===============================
BiocCheck('muSpaData_0.99.0.tar.gz')
===============================
── Installing muSpaData ────────────────────────────────────────────────────────
✖ ERROR: /tmp/RtmpTKVK4i/file19cc83d4792cf/muSpaData must be loadable.
✔ Package installed successfully
── muSpaData session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpTKVK4i/file19cc83d4792cf/muSpaData
→ BiocVersion: 3.21
→ Package: muSpaData
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3682/muSpaData_20250102162136/muSpaData.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpTKVK4i/file19cc83d4792cf/muSpaData
→ installDir: /tmp/RtmpTKVK4i/file19cc813cbd08c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on muSpaData ──────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 4.3 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ ExperimentData
* 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: SingleCellData
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 (67%).
* 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 muSpaData...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
Error: .onLoad failed in loadNamespace() for 'muSpaData', details:
call: createHubAccessors(pkgname, ts)
error: could not find function "createHubAccessors"
Execution halted