Issue with make rd - Githubissues

lgatto commented 7 years ago

I keep getting this weird error when running make rd with a couple of packages. Here's what happens for MSnbase with the latest github commit (08169a9c01170dfa875e1e875ccb88684f46f121). The Rstart-up message was removed:

make rd PKG=MSnbase
rm -rf MSnbase//src/*.o MSnbase/src/*.so
rm -rf MSnbase//*~
find . -name '.Rhistory' -exec rm '{}' \;
rm -rf MSnbase//vignettes/.\#*
rm -rf MSnbase//vignettes/\#*
rm -rf MSnbase.Rcheck
""/usr/local/lib64/R"/bin/R" -e "library(roxygen2); roxygenize('"MSnbase/"', roclets=\"rd\")";

[...]

> library(roxygen2); roxygenize('MSnbase/', roclets="rd")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
Loading required package: plyr
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:plyr’:

    rename

The following object is masked from ‘package:base’:

    expand.grid

Attaching package: ‘IRanges’

The following object is masked from ‘package:plyr’:

    desc

Loading required package: preprocessCore
Loading required package: vsn
Loading required package: grid
Loading required package: reshape2
Loading required package: affy

Attaching package: ‘affy’

The following object is masked from ‘package:ProtGenerics’:

    intensity

Loading required package: impute
Loading required package: pcaMethods

Attaching package: ‘pcaMethods’

The following object is masked from ‘package:stats’:

    loadings

Loading required package: mzID

Attaching package: ‘mzID’

The following object is masked from ‘package:plyr’:

    id

Loading required package: MALDIquant

This is MALDIquant version 1.16.1
Quantitative Analysis of Mass Spectrometry Data
 See ‘?MALDIquant’ for more information about this package.

Attaching package: ‘MALDIquant’

The following objects are masked from ‘package:affy’:

    intensity, intensity<-

The following objects are masked from ‘package:IRanges’:

    isEmpty, trim

The following object is masked from ‘package:S4Vectors’:

    isEmpty

The following objects are masked from ‘package:ProtGenerics’:

    intensity, mass, mz, mz<-

Loading required package: digest
Loading required package: lattice
Loading required package: ggplot2
Loading required package: XML
Loading required package: roxygen_devtest
Error in .requirePackage(package) : 
  unable to find required package ‘roxygen_devtest’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘roxygen_devtest’
Loading required package: roxygen_devtest
Error in .requirePackage(package) : 
  unable to find required package ‘roxygen_devtest’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘roxygen_devtest’
Error in setClassUnion("mzIDClasses", c("mzID", "mzIDCollection")) : 
  unable to create union class:  could not set members "mzID", "mzIDCollection"
Calls: roxygenize ... load_code -> lapply -> FUN -> eval -> eval -> setClassUnion
Execution halted
make: *** [rd] Error 1

Session information is

> sessionInfo()
R Under development (unstable) (2017-02-25 r72256)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/libf77blas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] MSnbase_2.1.10      ProtGenerics_1.7.0  BiocParallel_1.9.5 
[4] mzR_2.9.6           Rcpp_0.12.9         Biobase_2.35.1     
[7] BiocGenerics_0.21.3 roxygen2_6.0.1     

loaded via a namespace (and not attached):
 [1] msdata_0.15.1         compiler_3.4.0        BiocInstaller_1.25.3 
 [4] plyr_1.8.4            iterators_1.0.8       tools_3.4.0          
 [7] zlibbioc_1.21.0       digest_0.6.12         MALDIquant_1.16.1    
[10] tibble_1.2            preprocessCore_1.37.0 gtable_0.2.0         
[13] lattice_0.20-34       foreach_1.4.3         commonmark_1.2       
[16] stringr_1.2.0         xml2_1.1.1            IRanges_2.9.18       
[19] S4Vectors_0.13.15     stats4_3.4.0          grid_3.4.0           
[22] impute_1.49.0         R6_2.2.0              XML_3.98-1.5         
[25] limma_3.31.16         ggplot2_2.2.1         reshape2_1.4.2       
[28] magrittr_1.5          scales_0.4.1          pcaMethods_1.67.0    
[31] codetools_0.2-15      mzID_1.13.0           assertthat_0.1       
[34] colorspace_1.3-2      stringi_1.1.2         affy_1.53.0          
[37] doParallel_1.0.10     lazyeval_0.2.0        munsell_0.4.3        
[40] vsn_3.43.9

Note that running devtools::document("MSnbase") works and generates new rd files (see commit references above).

I have similar issues with pRoloc

Error in .requirePackage(package) : 
  unable to find required package ‘roxygen_devtest’
Calls: roxygenize ... makeClassRepresentation -> makeExtends -> .requirePackage
In addition: Warning messages:
1: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘MLInterfaces’ 
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘roxygen_devtest’
Execution halted
make: *** [rd] Error 1

But other packages work, and I couldn't find anything online. A new R and packages installation didn't help. I am not sure what to do now.

@sgibb - could you pull the latest MSnbase and try, please.

jorainer commented 7 years ago

Have you tried to install an older roxygen2 version? I had a similar error when just running roxygenize on xcms (i.e.

Error in .requirePackage(package) : 
  unable to find required package ‘roxygen_devtest’

I installed an older roxygen2 version (currently I have 5.0.1) and the error disappeared

lgatto commented 7 years ago

I don't even have roxygen installed. I have

> packageVersion("roxygen2")
[1] ‘6.0.1’

I also had the error with 5.0.1.

jorainer commented 7 years ago

I just pulled MSnbase and maker. I don't get the error:

jobook:git jo$ make rd PKG=MSnbase
rm -rf MSnbase//src/*.o MSnbase/src/*.so
rm -rf MSnbase//*~
find . -name '.Rhistory' -exec rm '{}' \;
rm -rf MSnbase//vignettes/.\#*
rm -rf MSnbase//vignettes/\#*
rm -rf MSnbase.Rcheck
""/Users/jo/R/R-3.4-devel-BioC3.5-devel/lib/R"/bin/R" -e "library(roxygen2); roxygenize('"MSnbase/"', roclets=\"rd\")";

R Under development (unstable) (2017-01-19 r72014) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.4.0/x86_64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(roxygen2); roxygenize('MSnbase/', roclets="rd")
Updating roxygen version in  /Users/jo/Projects/git/MSnbase/DESCRIPTION 
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
Loading required package: plyr
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:plyr’:

    rename

The following object is masked from ‘package:base’:

    expand.grid

Attaching package: ‘IRanges’

The following object is masked from ‘package:plyr’:

    desc

Loading required package: preprocessCore
Loading required package: vsn
Loading required package: grid
Loading required package: reshape2
Loading required package: affy

Attaching package: ‘affy’

The following object is masked from ‘package:ProtGenerics’:

    intensity

Loading required package: impute
Loading required package: pcaMethods

Attaching package: ‘pcaMethods’

The following object is masked from ‘package:stats’:

    loadings

Loading required package: mzID

Attaching package: ‘mzID’

The following object is masked from ‘package:plyr’:

    id

Loading required package: MALDIquant

This is MALDIquant version 1.16.1
Quantitative Analysis of Mass Spectrometry Data
 See ‘?MALDIquant’ for more information about this package.

Attaching package: ‘MALDIquant’

The following objects are masked from ‘package:affy’:

    intensity, intensity<-

The following objects are masked from ‘package:IRanges’:

    isEmpty, trim

The following object is masked from ‘package:S4Vectors’:

    isEmpty

The following objects are masked from ‘package:ProtGenerics’:

    intensity, mass, mz, mz<-

Loading required package: digest
Loading required package: lattice
Loading required package: ggplot2
Loading required package: XML
Creating a new generic function for ‘smooth’ in package ‘roxygen_devtest’
Creating a new generic function for ‘plotDensity’ in package ‘roxygen_devtest’
Creating a new generic function for ‘trimws’ in package ‘roxygen_devtest’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
Writing averageMSnSet.Rd
Writing aggvar.Rd
Writing featureCV.Rd
Writing nQuants.Rd
Writing commonFeatureNames.Rd
Writing selectFeatureData.Rd
Writing nFeatures.Rd
Writing iPQF.Rd
Writing imageNA2.Rd
Writing naplot.Rd
Writing makeNaData.Rd
Writing navMS.Rd
Writing MSnbaseOptions.Rd
Writing readMzTabData.Rd
Writing readMzTabData_v0.9.Rd
Writing get.amino.acids.Rd
Writing get.atomic.mass.Rd
Writing getVariableName.Rd
Writing grepEcols.Rd
Writing listOf.Rd
Writing npcv.Rd
Writing compareMSnSets.Rd
> 
>

My session info:

> sessionInfo()
R Under development (unstable) (2017-01-19 r72014)
Platform: x86_64-apple-darwin16.4.0/x86_64 (64-bit)
Running under: macOS Sierra 10.12.4

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] S4Vectors_0.13.13      MassSpecWavelet_1.41.0 waveslim_1.7.5        
 [4] multtest_2.31.0        RANN_2.5               plyr_1.8.4            
 [7] RColorBrewer_1.1-2     lattice_0.20-34        MSnbase_2.1.13        
[10] BiocParallel_1.9.5     Biobase_2.35.0         ProtGenerics_1.7.0    
[13] BiocGenerics_0.21.3    mzR_2.9.6              Rcpp_0.12.9           
[16] roxygen2_5.0.1        

loaded via a namespace (and not attached):
 [1] compiler_3.4.0        BiocInstaller_1.25.3  iterators_1.0.8      
 [4] tools_3.4.0           zlibbioc_1.21.0       digest_0.6.12        
 [7] MALDIquant_1.16.1     tibble_1.2            preprocessCore_1.37.0
[10] gtable_0.2.0          Matrix_1.2-8          foreach_1.4.3        
[13] stringr_1.1.0         IRanges_2.9.18        grid_3.4.0           
[16] impute_1.49.0         survival_2.40-1       XML_3.98-1.5         
[19] limma_3.31.11         ggplot2_2.2.1         reshape2_1.4.2       
[22] magrittr_1.5          MASS_7.3-45           splines_3.4.0        
[25] scales_0.4.1          pcaMethods_1.67.0     codetools_0.2-15     
[28] assertthat_0.1        mzID_1.13.0           colorspace_1.3-2     
[31] stringi_1.1.2         affy_1.53.0           lazyeval_0.2.0       
[34] munsell_0.4.3         doParallel_1.0.10     vsn_3.43.7           
[37] affyio_1.45.0        
>

jorainer commented 7 years ago

I update roxygen2 to 6.0.1 and boom:

jobook:git jo$ make rd PKG=MSnbase
rm -rf MSnbase//src/*.o MSnbase/src/*.so
rm -rf MSnbase//*~
find . -name '.Rhistory' -exec rm '{}' \;
rm -rf MSnbase//vignettes/.\#*
rm -rf MSnbase//vignettes/\#*
rm -rf MSnbase.Rcheck
""/Users/jo/R/R-3.4-devel-BioC3.5-devel/lib/R"/bin/R" -e "library(roxygen2); roxygenize('"MSnbase/"', roclets=\"rd\")";

R Under development (unstable) (2017-01-19 r72014) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.4.0/x86_64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(roxygen2); roxygenize('MSnbase/', roclets="rd")
Updating roxygen version in /Users/jo/Projects/git/MSnbase/DESCRIPTION
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
Loading required package: plyr
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:plyr’:

    rename

The following object is masked from ‘package:base’:

    expand.grid

Attaching package: ‘IRanges’

The following object is masked from ‘package:plyr’:

    desc

Loading required package: preprocessCore
Loading required package: vsn
Loading required package: grid
Loading required package: reshape2
Loading required package: affy

Attaching package: ‘affy’

The following object is masked from ‘package:ProtGenerics’:

    intensity

Loading required package: impute
Loading required package: pcaMethods

Attaching package: ‘pcaMethods’

The following object is masked from ‘package:stats’:

    loadings

Loading required package: mzID

Attaching package: ‘mzID’

The following object is masked from ‘package:plyr’:

    id

Loading required package: MALDIquant

This is MALDIquant version 1.16.1
Quantitative Analysis of Mass Spectrometry Data
 See ‘?MALDIquant’ for more information about this package.

Attaching package: ‘MALDIquant’

The following objects are masked from ‘package:affy’:

    intensity, intensity<-

The following objects are masked from ‘package:IRanges’:

    isEmpty, trim

The following object is masked from ‘package:S4Vectors’:

    isEmpty

The following objects are masked from ‘package:ProtGenerics’:

    intensity, mass, mz, mz<-

Loading required package: digest
Loading required package: lattice
Loading required package: ggplot2
Loading required package: XML
Loading required package: roxygen_devtest
Error in .requirePackage(package) : 
  unable to find required package ‘roxygen_devtest’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘roxygen_devtest’
Loading required package: roxygen_devtest
Error in .requirePackage(package) : 
  unable to find required package ‘roxygen_devtest’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘roxygen_devtest’
Error in setClassUnion("mzIDClasses", c("mzID", "mzIDCollection")) : 
  unable to create union class:  could not set members "mzID", "mzIDCollection"
Calls: roxygenize ... load_code -> lapply -> FUN -> eval -> eval -> setClassUnion
Execution halted
make: *** [rd] Error 1
jobook:git jo$

lgatto commented 7 years ago

That's a relief - I was afraid I had some dependencies issue. Thank you!

ComputationalProteomicsUnit / maker

Issue with make rd #28