Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘scDDboost/DESCRIPTION’ ... OK
* preparing ‘scDDboost’:
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
 OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
* cleaning src
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
* 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 ‘scDDboost_0.99.14.tar.gz’

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 BiocCheckGitClone('scDDboost')

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Error: package or namespace load failed for ‘BiocCheck’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘biocViews’
Execution halted




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2349/f92cd91c38af33459e5adeb9dc29e3bb3eaf6cc9/scDDboost.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDDboost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDDboost’ version ‘0.99.14’
* 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 serialization versions ... OK
* checking whether package ‘scDDboost’ can be installed ... [95s/95s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [39s/39s] OK
* checking Rd files ... [1s/1s] 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘scDDboost/libs/scDDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [188s/70s] OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
scDDboost-package 39.466  4.247  15.269
detK              37.212  4.155  13.618
PDD               36.688  4.455  15.524
cal_D             30.183  3.413   8.696
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [72s/72s]
 [73s/73s] OK
* 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 ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2349/f92cd91c38af33459e5adeb9dc29e3bb3eaf6cc9/scDDboost.Rcheck/00check.log’
for details.






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 BiocCheck('scDDboost_0.99.14.tar.gz')

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This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
  cmd: /Library/Frameworks/R.framework/Resources/bin/R
  args: --vanilla -e 'library(scDDboost)'
  stderr:
  Loading required package: ggplot2
  Error: package or namespace load failed for ‘scDDboost’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
   there is no package called ‘SummarizedExperiment’
  Execution halted

    * ERROR:
      /Users/pkgbuild/packagebuilder/workers/jobs/2349/f92cd91c38af33459e5adeb9dc29e3bb3eaf6cc9/scDDboost_0.99.14.tar.gz
      must be loadable.
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2349/f92cd91c38af33459e5adeb9dc29e3bb3eaf6cc9/scDDboost_0.99.14.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpBGuKRY/file596f282b2d95/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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...
* 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 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...
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
* Checking License: for restrictive use...
    * NOTE: License 'GPL (>= 2)' unknown; licenses cannot restrict use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scDDboost...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
        suppressWarnings() in R/rwMLE.R (line 18, column 13)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 1 functions > 50 lines.
      The longest 5 functions are:
        PDD() (R/PDD.R, line 26): 132 lines
        PDD_random() (R/PDD_random.R, line 18): 44 lines
        cal_D() (R/cal_D.R, line 12): 39 lines
        detK() (R/detK.R, line 13): 27 lines
        g_cl() (R/g_cl.R, line 7): 25 lines
* Checking man page documentation...
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘SummarizedExperiment’
Calls: BiocCheck ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir scDDboost_0.99.14.tar.gz'
>>>>>>> 

ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘scDDboost’
* removing ‘/Users/pkgbuild/packagebuilder/workers/jobs/2349/f92cd91c38af33459e5adeb9dc29e3bb3eaf6cc9/libdir/scDDboost’