Search
Question: Unable to install BiocStyle: not available (for R version 3.5.0)
0
gravatar for nereidaramirez
5 months ago by
nereidaramirez0 wrote:

Yesterday I was walking through this tutorial and I was able to run every package, but when I tried to execute the script today I wasn't able to load libraries that I had already installed (e.g. BiocStyle and GenomicFeatures). The error that I keep getting is attached below. Thus far I've tried every suggestion on this thread but nothing has worked. Is there anyway to restore these packages in R 3.5.0? 

 

> install.packages("BiocStyle", repos="https://bioconductor.org/biocLite.R", dependencies=TRUE)

Installing package into ‘C:/Users/KimLab/Documents/R/win-library/3.5’

(as ‘lib’ is unspecified)

Warning in install.packages :

  unable to access index for repository https://bioconductor.org/biocLite.R/src/contrib:

  cannot open URL 'https://bioconductor.org/biocLite.R/src/contrib/PACKAGES'

Warning in install.packages :

  package ‘BiocStyle’ is not available (for R version 3.5.0)

Warning in install.packages :

  unable to access index for repository https://bioconductor.org/biocLite.R/bin/windows/contrib/3.5:

  cannot open URL 'https://bioconductor.org/biocLite.R/bin/windows/contrib/3.5/PACKAGES'


> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17                locfit_1.5-9.1             
 [3] lattice_0.20-35             assertthat_0.2.0           
 [5] digest_0.6.15               SingleCellExperiment_1.2.0 
 [7] mime_0.5                    R6_2.2.2                   
 [9] GenomeInfoDb_1.16.0         plyr_1.8.4                 
[11] stats4_3.5.0                ggplot2_2.2.1              
[13] pillar_1.2.3                zlibbioc_1.26.0            
[15] rlang_0.2.0                 lazyeval_0.2.1             
[17] data.table_1.11.2           S4Vectors_0.18.2           
[19] Matrix_1.2-14               BiocParallel_1.14.1        
[21] RCurl_1.95-4.10             munsell_0.4.3              
[23] shiny_1.1.0                 DelayedArray_0.6.0         
[25] compiler_3.5.0              httpuv_1.4.3               
[27] vipor_0.4.5                 pkgconfig_2.0.1            
[29] BiocGenerics_0.26.0         ggbeeswarm_0.6.0           
[31] htmltools_0.3.6             tidyselect_0.2.4           
[33] SummarizedExperiment_1.10.1 tibble_1.4.2               
[35] gridExtra_2.3               GenomeInfoDbData_1.1.0     
[37] edgeR_3.22.2                IRanges_2.14.10            
[39] matrixStats_0.53.1          viridisLite_0.3.0          
[41] dplyr_0.7.5                 later_0.7.2                
[43] bitops_1.0-6                grid_3.5.0                 
[45] xtable_1.8-2                gtable_0.2.0               
[47] magrittr_1.5                scales_0.5.0               
[49] XVector_0.20.0              viridis_0.5.1              
[51] promises_1.0.1              bindrcpp_0.2.2             
[53] limma_3.36.1                DelayedMatrixStats_1.2.0   
[55] tools_3.5.0                 Biobase_2.40.0             
[57] glue_1.2.0                  beeswarm_0.2.3             
[59] purrr_0.2.4                 parallel_3.5.0             
[61] yaml_2.1.19                 colorspace_1.3-2           
[63] GenomicRanges_1.32.3        shinydashboard_0.7.0       
[65] bindr_0.1.1              

 

ADD COMMENTlink modified 5 months ago by Mike Smith3.0k • written 5 months ago by nereidaramirez0
1
gravatar for Mike Smith
5 months ago by
Mike Smith3.0k
EMBL Heidelberg / de.NBI
Mike Smith3.0k wrote:

If you already have packages installed, there should be no need to install them again.  You can just load them with library() e.g.

library(BiocStyle)

If you do need to install a new package, it's a more typical use case to install Bioconductor packages with biocLite(). Do you get the same errors with this?

BiocInstaller::biocLite('BiocStyle')
ADD COMMENTlink modified 5 months ago • written 5 months ago by Mike Smith3.0k

Yes I do still get errors: 

 

> BiocInstaller::biocLite('BiocStyle')

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).

Installing package(s) ‘BiocStyle’

trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/BiocStyle_2.8.1.zip'

Content type 'application/zip' length 754238 bytes (736 KB)

downloaded 736 KB

package ‘BiocStyle’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\KimLab\AppData\Local\Temp\Rtmpo9sorg\downloaded_packages

installation path not writeable, unable to update packages: MASS, survival

Old packages: 'data.table', 'openxlsx', 'rrcov', 'simpleSingleCell', 'utf8'

Update all/some/none? [a/s/n]: 

a

also installing the dependency ‘zip’

  There are binary versions available but the source versions are later:

           binary source needs_compilation

data.table 1.11.2 1.11.4              TRUE

openxlsx   4.0.17  4.1.0              TRUE

  Binaries will be installed

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/zip_1.0.0.zip'

Content type 'application/zip' length 104827 bytes (102 KB)

downloaded 102 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/data.table_1.11.2.zip'

Content type 'application/zip' length 1825285 bytes (1.7 MB)

downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/openxlsx_4.0.17.zip'

Content type 'application/zip' length 2427142 bytes (2.3 MB)

downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rrcov_1.4-4.zip'

Content type 'application/zip' length 1662044 bytes (1.6 MB)

downloaded 1.6 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/utf8_1.1.4.zip'

Content type 'application/zip' length 214628 bytes (209 KB)

downloaded 209 KB

package ‘zip’ successfully unpacked and MD5 sums checked

package ‘data.table’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘data.table’

package ‘openxlsx’ successfully unpacked and MD5 sums checked

package ‘rrcov’ successfully unpacked and MD5 sums checked

package ‘utf8’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\KimLab\AppData\Local\Temp\Rtmpo9sorg\downloaded_packages

installing the source package ‘simpleSingleCell’

trying URL 'https://bioconductor.org/packages/3.7/workflows/src/contrib/simpleSingleCell_1.2.1.tar.gz'

Content type 'application/x-gzip' length 16035226 bytes (15.3 MB)

downloaded 15.3 MB

* installing *source* package 'simpleSingleCell' ...

** inst

** help

No man pages found in package  'simpleSingleCell' 

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

*** arch - i386

Error: package or namespace load failed for 'BiocStyle' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

 there is no package called 'stringi'

Error : package 'BiocStyle' could not be loaded

Error: loading failed

Execution halted

*** arch - x64

Error: package or namespace load failed for 'BiocStyle' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

 there is no package called 'stringi'

Error : package 'BiocStyle' could not be loaded

Error: loading failed

Execution halted

ERROR: loading failed for 'i386', 'x64'

* removing 'C:/Users/KimLab/Documents/R/win-library/3.5/simpleSingleCell'

* restoring previous 'C:/Users/KimLab/Documents/R/win-library/3.5/simpleSingleCell'

In R CMD INSTALL

The downloaded source packages are in

‘C:\Users\KimLab\AppData\Local\Temp\Rtmpo9sorg\downloaded_packages’

Warning message:

In install.packages(update[instlib == l, "Package"], l, repos = repos,  :

  installation of package ‘simpleSingleCell’ had non-zero exit status


 

ADD REPLYlink modified 4 months ago • written 4 months ago by nereidaramirez0
​And when I try to load the library: 
> library(BiocStyle)

Error: package or namespace load failed for ‘BiocStyle’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

 there is no package called ‘stringi’
ADD REPLYlink written 4 months ago by nereidaramirez0

Install the missing dependency BiocInstaller::biocLite("stringi") ; it's not really clear why stringi is (no longer) installed.

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 22k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 372 users visited in the last hour