Bioconductor Single Package Builder - Build History

===============================

 R CMD BUILD

===============================

* checking for file ‘ceRNAR/DESCRIPTION’ ... OK
* preparing ‘ceRNAR’:
* 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 ‘ceRNAR_0.99.17.tar.gz’

===============================

 BiocCheckGitClone('ceRNAR')

===============================

─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: ceRNAR
─ PackageVersion: 0.99.17
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2847/b975c4b2afcbc14364925952519ced035da4a58f/ceRNAR
─ 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...
    * ERROR: Use Authors@R field not Author/Maintainer fields. Do not
      use both.
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2847/b975c4b2afcbc14364925952519ced035da4a58f/ceRNAR.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ceRNAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ceRNAR’ version ‘0.99.17’
* 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 ‘ceRNAR’ 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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘biomaRt’ ‘ggpubr’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [19s/20s] OK
* checking whether the package can be loaded with stated dependencies ... [18s/19s] WARNING


##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Error: package or namespace load failed for ‘ceRNAR’ in namespaceExport(ns, exports):
 undefined exports: All_steps_interface, SegmentClusteringPlusPeakMerging, ceRNACustomize, ceRNAFunction, ceRNAIntegrate, ceRNALocation, ceRNAMethod, ceRNAModule, ceRNASurvival, ceRNATCGA, ceRNAValidate, ceRNApairFilering, ceRNAputativePairs
Execution halted

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... [0s/0s] WARNING
Error in library(ceRNAR) : there is no package called ‘ceRNAR’
Calls: suppressMessages -> withCallingHandlers -> library
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] WARNING
Error in loadNamespace("ceRNAR") : there is no package called ‘ceRNAR’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
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 in loadNamespace("ceRNAR") : there is no package called ‘ceRNAR’
Calls: suppressMessages ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking loading without being on the library search path ... [0s/0s] WARNING
Error in library(ceRNAR, lib.loc = "/Users/pkgbuild/packagebuilder/workers/jobs/2847/R-libs") : 
  there is no package called ‘ceRNAR’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
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 in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [3s/3s] NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
Error in loadNamespace(name) : there is no package called ‘ceRNAR’
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd line widths ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: suppressPackageStartupMessages ... withCallingHandlers -> <Anonymous> -> Rd_db -> find.package
Execution halted
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Warning in gzfile(file, "rb") :
  cannot open compressed file '', probable reason 'No such file or directory'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> readRDS -> gzfile
Execution halted
* checking for missing documentation entries ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> dirname -> find.package
Execution halted
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
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
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 ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Calls: <Anonymous> -> find.package
Execution halted
* checking for unstated dependencies in examples ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Execution halted
* checking contents of ‘data’ directory ... WARNING
Output for data("gene_exp", package = "ceRNAR"):
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called ‘ceRNAR’
  Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
  Execution halted
Output for data("mirna_exp", package = "ceRNAR"):
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called ‘ceRNAR’
  Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
  Execution halted
Output for data("surv_data", package = "ceRNAR"):
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called ‘ceRNAR’
  Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
  Execution halted
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘ceRNAR’
Execution halted
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [6s/6s] OK
* DONE

Status: 15 WARNINGs, 6 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2847/b975c4b2afcbc14364925952519ced035da4a58f/ceRNAR.Rcheck/00check.log’
for details.






===============================

 BiocCheck('ceRNAR_0.99.17.tar.gz')

===============================

─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: ceRNAR
─ PackageVersion: 0.99.17
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpGYiAxZ/file9ecd4e8feef2/ceRNAR
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpGYiAxZ/file9ecd7a444080
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2847/b975c4b2afcbc14364925952519ced035da4a58f/ceRNAR.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 4.2.0 to 4.3.0.
* 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:
      Network, Clustering
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...


##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
    * WARNING: Import Biobase, biomaRt in NAMESPACE as well as
      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 ceRNAR...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 26 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 453 lines (12%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1328 lines
      (35%) 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 name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 12 NOTES

See the ceRNAR.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ceRNAR_0.99.17.tar.gz'
>>>>>>> 

* installing *source* package ‘ceRNAR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ceRNAR)