Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* preparing ‘RNAseqCovarImpute’:
* 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
  NB: this package now depends on R (>= 3.5.0)
  WARNING: Added dependency on R >= 3.5.0 because serialized objects in
  serialize/load version 3 cannot be read in older versions of R.
  File(s) containing such objects:
    ‘RNAseqCovarImpute/data/RNAseqCovarImpute_data.RData’
* building ‘RNAseqCovarImpute_0.99.3.tar.gz’

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 BiocCheckGitClone('RNAseqCovarImpute')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: RNAseqCovarImpute
─ PackageVersion: 0.99.3
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3021/53d16ab22bb651ef137f3c7dae8b40316270b0e8/RNAseqCovarImpute
─ 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...
* Checking CITATION...

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

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




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3021/53d16ab22bb651ef137f3c7dae8b40316270b0e8/RNAseqCovarImpute.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 ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* this is package ‘RNAseqCovarImpute’ version ‘0.99.3’
* 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 ‘RNAseqCovarImpute’ 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 ... OK
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
* checking whether the package can be unloaded cleanly ... [2s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [11s/12s] NOTE
combine_rubins: no visible binding for global variable ‘i’
combine_rubins: no visible binding for global variable ‘coef_combined’
combine_rubins: no visible binding for global variable ‘rubins_t_bayes’
combine_rubins: no visible binding for global variable ‘combined_p’
combine_rubins: no visible binding for global variable
  ‘combined_p_bayes’
get_gene_bin_intervals: no visible binding for global variable ‘end’
get_gene_bin_intervals: no visible binding for global variable ‘start’
impute_by_gene_bin: no visible binding for global variable ‘i’
impute_by_gene_bin_parallel: no visible binding for global variable ‘i’
limmavoom_imputed_data_list: no visible binding for global variable
  ‘gene_bin’
limmavoom_imputed_data_list: no visible binding for global variable ‘i’
limmavoom_imputed_data_list_parallel: no visible binding for global
  variable ‘gene_bin’
limmavoom_imputed_data_list_parallel: no visible binding for global
  variable ‘i’
lowess_all_gene_bins: no visible binding for global variable ‘gene_bin’
lowess_all_gene_bins: no visible binding for global variable ‘i’
voom_master_lowess: no visible global function definition for ‘is’
voom_master_lowess: no visible global function definition for ‘new’
voom_master_lowess: no visible global function definition for ‘lowess’
voom_master_lowess: no visible global function definition for
  ‘approxfun’
voom_sx_sy: no visible global function definition for ‘is’
voom_sx_sy: no visible global function definition for ‘new’
Undefined global functions or variables:
  approxfun coef_combined combined_p combined_p_bayes end gene_bin i is
  lowess new rubins_t_bayes start
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "approxfun", "end", "lowess", "start")
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 ... WARNING
Undocumented data sets:
  ‘example_DGE’ ‘example_data’
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 ... 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                               old_size new_size compress
  RNAseqCovarImpute_data.RData    436Kb    245Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/37s] ERROR
Running examples in ‘RNAseqCovarImpute-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: impute_by_gene_bin_parallel
> ### Title: impute_by_gene_bin_parallel
> ### Aliases: impute_by_gene_bin_parallel
> 
> ### ** Examples
> 
> data(RNAseqCovarImpute_data)
> intervals <- get_gene_bin_intervals(example_DGE, example_data, n = 10)
> gene_bin_impute <- impute_by_gene_bin_parallel(example_data,
+     intervals,
+     example_DGE,
+     m = 2,
+     cores = 2
+ )
> coef_se <- limmavoom_imputed_data_list_parallel(
+     gene_intervals = intervals,
+     DGE = example_DGE,
+     imputed_data_list = gene_bin_impute,
+     m = 2,
+     voom_formula = "~x + y + z + a + b",
+     predictor = "x",
+     cores = 2
+ )
> 
> final_res <- combine_rubins(
+     DGE = example_DGE,
+     model_results = coef_se,
+     voom_formula = "~x + y + z + a + b"
+ )
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("impute_by_gene_bin_parallel", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (<-localhost:11970)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 4 (<-localhost:11970)
Error: connections left open:
	<-localhost:11970 (sockconn)
	<-localhost:11970 (sockconn)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* 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/7s] OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3021/53d16ab22bb651ef137f3c7dae8b40316270b0e8/RNAseqCovarImpute.Rcheck/00check.log’
for details.





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 BiocCheck('RNAseqCovarImpute_0.99.3.tar.gz')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: RNAseqCovarImpute
─ PackageVersion: 0.99.3
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpIlalVw/file2c3f1ac2b856/RNAseqCovarImpute
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpIlalVw/file2c3f4a7c25df
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3021/53d16ab22bb651ef137f3c7dae8b40316270b0e8/RNAseqCovarImpute.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 3.5.0 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:
      Bayesian
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...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* 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...
    * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Loading required namespace: stringr
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RNAseqCovarImpute...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 4 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; 167 lines (10%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 33 lines (2%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 225 lines
      (13%) 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 | 0 WARNINGS | 10 NOTES

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

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir RNAseqCovarImpute_0.99.3.tar.gz'
>>>>>>> 

* installing *source* package ‘RNAseqCovarImpute’ ...
** 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 (RNAseqCovarImpute)