Question

How to launch the RnBeads Data Juggler?

0

Entering edit mode

Federica ▴ 10

@federica-24874

Last seen 3.6 years ago

Italy

Hi,

I have problems with RnBeads. In particular, It does not work the rnb.run.dj() command to open RnBeads Data Juggler.

RnBeads team said me to install the last version of RnBeads package through the following link:

https://bioconductor.org/packages/3.13/bioc/html/RnBeads.html

However, I still have problems, also after installing the last R version "4.1" for the last release of RnBeads.

I run the following commands:

  if (!requireNamespace("BiocManager", quietly = TRUE))  
  install.packages("BiocManager")
 # The following initializes usage of Bioc devel BiocManager::install(version='devel')
  BiocManager::install("RnBeads")

After, I tried to load RnBeads with:

library(RnBeads)

And in R console, I found:

 namespace for "ggplot2" in loadNamespace (j <- i [[1L]], c (lib.loc,.libPaths ()), versionCheck = vI [[j]]):  there is no package called 'pillar' 
Error: Package "ggplot2" could not be loaded

Therefore, I cannot use rnb.run.dj() to launch RnBeads Data Juggler, since R does not find the function.

Might someone help me? Thank u!

sessionInfo():

     R Under development (unstable) (2021-02-23 r80032) Platform:
     x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build
     19042)

     Matrix products: default

     locale: [1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
     LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C                  
     LC_TIME=Italian_Italy.1252    

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

     other attached packages:  [1] fields_11.6          spam_2.6-0         
     dotCall64_1.0-1      ff_4.0.4             bit_4.0.4           
     cluster_2.1.1        MASS_7.3-53.1         [8] GenomicRanges_1.43.3
     GenomeInfoDb_1.27.6  IRanges_2.25.6       S4Vectors_0.29.7    
     BiocGenerics_0.37.1 

     loaded via a namespace (and not attached):  [1] compiler_4.1.0        
     BiocManager_1.30.10    XVector_0.31.1         bitops_1.0-6          
     tools_4.1.0            zlibbioc_1.37.0         [7] lifecycle_1.0.0    
     gtable_0.3.0           rlang_0.4.10           GenomeInfoDbData_1.2.4
     maps_3.3.0             glue_1.4.2             [13] R6_2.5.0           
     magrittr_2.0.1         scales_1.1.1           ellipsis_0.3.1        
     colorspace_2.0-0       RCurl_1.98-1.2         [19] munsell_0.5.0

RnBeads • 1.5k views

ADD COMMENT • link 3.8 years ago Federica ▴ 10

score 1 · Answer 1 · 2021-02-24

1

Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 7 days ago

United States

The hint is this part:

there is no package called 'pillar'

Which you can fix by doing

BiocManager::install("pillar")

ADD COMMENT • link 3.8 years ago James W. MacDonald 67k

0

Entering edit mode

I've followed your advice, so I've run:

BiocManager::install("pillar")

In Rstudio console, I've found:

Bioconductor version 3.13 (BiocManager 1.30.10), R Under development (unstable) (2021-02-23 r80032)
Installing package (s) 'pillar'
the dependency 'utf8' is also installed


  There is a binary version available, but the source version is later:
       binary source needs_compilation
pillar 1.4.7 1.5.0 FALSE

The package is available only in source form and requires compilation of C / C ++ / Fortran code: 'utf8'
  These will not be installed
'pillar' source package installation

opening URL 'https://cran.rstudio.com/src/contrib/pillar_1.5.0.tar.gz'
Content type 'application / x-gzip' length 1073627 bytes (1.0 MB)
downloaded 1.0 MB

ERROR: dependency 'utf8' is not available for package 'pillar'
* removing 'C: /Users/feder/Documents/R/win-library/4.1/pillar'

The downloaded source packages are in
'C: \ Users \ feder \ AppData \ Local \ Temp \ RtmpG2Hedz \ downloaded_packages'
Old packages: 'pkgload'
Update all / some / none? [a / s / n]:
to

  There is a binary version available, but the source version is later:
        binary source needs_compilation
pkgload 1.1.0 1.2.0 TRUE

  Binaries will be installed
opening URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/pkgload_1.1.0.zip'
Content type 'application / zip' length 163409 bytes (159 KB)
downloaded 159 KB

package 'pkgload' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C: \ Users \ feder \ AppData \ Local \ Temp \ RtmpG2Hedz \ downloaded_packages
Warning message:
In install.packages (...):
  installation of package 'pillar' had non-zero exit status

So, I suppose that now the problem is the dependency utf8...but I wouldn't know how to overcome it...

Thank u for your help and time!

ADD REPLY • link 3.8 years ago Federica ▴ 10

1

Entering edit mode

You need to install Rtools to be able to compile source packages. After which it works fine:


> install("pillar")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'pillar'

  There is a binary version available but the source version is later:
       binary source needs_compilation
pillar  1.4.7  1.5.0             FALSE

installing the source package 'pillar'

trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.5.0.tar.gz'
Content type 'application/x-gzip' length 1073627 bytes (1.0 MB)
downloaded 1.0 MB

* installing *source* package 'pillar' ...
** package 'pillar' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pillar'
    finding HTML links ... done
    align                                   html  
    colonnade                               html  
    ctl_new_pillar                          html  
    deprecated                              html  
    dim_desc                                html  
    expect_known_display                    html  
    extra_cols                              html  
    format_tbl                              html  
    format_type_sum                         html  
    get_extent                              html  
    glimpse                                 html  
    new_ornament                            html  
    finding level-2 HTML links ... done

    new_pillar                              html  
    new_pillar_component                    html  
    new_pillar_shaft                        html  
    new_pillar_title                        html  
    new_pillar_type                         html  
    new_tbl_format_setup                    html  
    pillar-package                          html  
    pillar                                  html  
    pillar_shaft                            html  
    squeeze                                 html  
    style_subtle                            html  
    tbl_format_body                         html  
    tbl_format_footer                       html  
    tbl_format_header                       html  
    tbl_format_setup                        html  
    tbl_sum                                 html  
    type_sum                                html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (pillar)