WCGNA installation help

Question

[prekrish]

Hi,

I am trying to install WCGNA (1.67) package in R 3.6.0 and have not been successful in doing so. First, I tried to install Bioconductor -

if (!requireNamespace("BiocManager", quietly = TRUE))
                         install.packages("BiocManager") BiocManager::install()

This was the output for the above command -

Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'BiocVersion'

I first tried automatic installation of WCGNA using the command BiocManager::install("WCGNA") but got the following warning message -

Warning message:
package ‘WCGNA’ is not available (for R version 3.6.0)

Then I tried manual installation of WCGNA using the command - install.packages("WCGNA", repos = NULL, lib=.Library). This was the error message that I got -

Error in install.packages("WCGNA", repos = NULL, lib = .Library) : 
  type == "both" cannot be used with 'repos = NULL' .

I am not sure I understand this error message.

I also tried installing WCGNA in R 3.5 but I am getting the same error message that package WCGNA is not available. I do not know where I am going wrong and it would be of great help if you can help me with this. I am using Windows computer.

Thank you very much

[Ram]

Please read the how-to on post types. This is a Question, not a Tool.

Remember, if you're looking for a tool or for help with a tool, you have a Question, not a Tool - it's commonly confused, but please be informed of the difference.

I'm making the necessary change now, but please be more careful in the future. Also, please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[Ram]

The error message are clear - please read them and Google them (and read the manual as well). The package is not yet available for R 3.6.0 and you cannot use install.packages(..., type="both",...) (probably picked by default in your case) when you use repos = NULL. Try type='source' instead.

[prekrish]

Thank you very much for your reply. I tried uninstalling R and reinstalled R 3.5.1. I then tried automatic installation of WCGNA using the following commands :

install.packages("BiocManager") 
BiocManager::install("WGCNA")

This was the output -

package 'WGCNA' successfully unpacked and MD5 sums checked 
                                  In R CMD INSTALL

However, when I gave the command - library(WCGNA) , I got the following error message - Error in library(WCGNA) : there is no package called ‘WCGNA’

I did not change any default parameters and installed in the default folder in Windows OS.

I also tried manual installation of WCGNA but I got the following error message -

Warning in install.packages("C:/Users/User/Documents/WGCNA_1.67.zip", repos = NULL,  :
  'lib = "C:/Users/User/Documents/WGCNA_1.67.zip"' is not writable

I am the administrator for the system and I don't quite understand where exactly I am going wrong. It would be of tremendous help if you can help me in this regard.

[Ram]

successfully unpacked is not successfully installed. Can you please paste the full output of install.packages("BiocManager"); BiocManager::install("WGCNA")?

If your R was installed and is managed by conda, I've seen many package installations fail. The way to install them if you're using conda would be to search for the package and install it using conda. In this case, that would be conda install -c bioconda r-WGCNA

Also, the command install.packages('<path_to_a_zip_file>, ...) does not make sense to me, given that install.packages expects package names, not a string it cannot decipher as a package name.

[prekrish]

Hi,

I'm using Windows OS. So I don't think I use conda. I'm not sure though. I tried installing R 3.4.3 and bioconductor 3.6. I then tried installing WCGNA and following is the output:

> biocLite("WCGNA")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘WCGNA’
Old packages: 'cluster', 'digest', 'nlme'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions are later:
         binary  source needs_compilation
cluster   2.0.8   2.0.9              TRUE
digest   0.6.18  0.6.19              TRUE
nlme    3.1-137 3.1-140              TRUE

  Binaries will be installed
trying URL 'https://mirrors.nics.utk.edu/cran/bin/windows/contrib/3.4/cluster_2.0.8.zip'
Content type 'application/zip' length 588040 bytes (574 KB)
downloaded 574 KB

trying URL 'https://mirrors.nics.utk.edu/cran/bin/windows/contrib/3.4/digest_0.6.18.zip'
Content type 'application/zip' length 176442 bytes (172 KB)
downloaded 172 KB

trying URL 'https://mirrors.nics.utk.edu/cran/bin/windows/contrib/3.4/nlme_3.1-137.zip'
Content type 'application/zip' length 2344000 bytes (2.2 MB)
downloaded 2.2 MB

package ‘cluster’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\User\AppData\Local\Temp\RtmpCeiQdJ\downloaded_packages
Warning message:
package ‘WCGNA’ is not available (for R version 3.4.3)

I am getting the same error message no matter what version of R i install. Should I do something different ? Thank you so much.

[Ram]

I'm using Windows OS. So I don't think I use conda.

OS has nothing to do with conda. In fact, ease of use across OS's is one of the reasons to use conda. Also, you have a typo: It's WGCNA, not WCGNA :-)

[prekrish]

Hi,

Thank you very much for your reply. I am not familiar with conda and also not quite well versed with R. I am learning how to do analysis using R. Would it be possible for you to explain what I have to do. Should I download something for this ?

[Ram]

Did you try biocLite('WGCNA')?

[prekrish]

Yes. I tried biocLite('WCGNA') and I am getting the same output :

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite('WCGNA')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘WCGNA’
Old packages: 'checkmate', 'cluster', 'digest', 'dplyr', 'fields', 'ggrepel',
  'hexbin', 'nlme', 'openssl', 'RcppArmadillo', 'robustbase', 'tibble'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions are later:
                   binary      source needs_compilation
checkmate           1.9.1       1.9.3              TRUE
cluster             2.0.8       2.0.9              TRUE
digest             0.6.18      0.6.19              TRUE
dplyr             0.8.0.1       0.8.1              TRUE
fields                9.7       9.8-3              TRUE
ggrepel             0.8.0       0.8.1              TRUE
hexbin             1.27.2      1.27.3              TRUE
nlme              3.1-137     3.1-140              TRUE
openssl               1.3         1.4              TRUE
RcppArmadillo 0.9.300.2.0 0.9.400.3.0              TRUE
robustbase         0.93-4      0.93-5              TRUE
tibble              2.1.1       2.1.2              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/checkmate_1.9.1.zip'
Content type 'application/zip' length 735324 bytes (718 KB)
downloaded 718 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/cluster_2.0.8.zip'
Content type 'application/zip' length 588040 bytes (574 KB)
do

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/digest_0.6.18.zip'
Content type 'application/zip' length 176442 bytes (172 KB)
downloaded 172 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/dplyr_0.8.0.1.zip'
Content type 'application/zip' length 3029353 bytes (2.9 MB)
downloaded 2.9 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/fields_9.7.zip'
Content type 'application/zip' length 3616587 bytes (3.4 MB)
downloaded 3.4 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/ggrepel_0.8.0.zip'
Content type 'application/zip' length 802374 bytes (783 KB)
downloaded 783 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/hexbin_1.27.2.zip'
Content type 'application/zip' length 685044 bytes (668 KB)
downloaded 668 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/nlme_3.1-137.zip'
Content type 'application/zip' length 2344000 bytes (2.2 MB)
downloaded 2.2 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/openssl_1.3.zip'
Content type 'application/zip' length 3907029 bytes (3.7 MB)
downloaded 3.7 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/RcppArmadillo_0.9.300.2.0.zip'
Content type 'application/zip' length 2241393 bytes (2.1 MB)
downloaded 2.1 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/robustbase_0.93-4.zip'
Content type 'application/zip' length 3227050 bytes (3.1 MB)
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/tibble_2.1.1.zip'
Content type 'application/zip' length 238931 bytes (233 KB)
downloaded 233 KB

package ‘checkmate’ successfully unpacked and MD5 sums checked
package ‘cluster’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘dplyr’ successfully unpacked and MD5 sums checked
package ‘fields’ successfully unpacked and MD5 sums checked
package ‘ggrepel’ successfully unpacked and MD5 sums checked
package ‘hexbin’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘openssl’ successfully unpacked and MD5 sums checked
package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
package ‘robustbase’ successfully unpacked and MD5 sums checked
package ‘tibble’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\prekrish\AppData\Local\Temp\RtmpquszbY\downloaded_packages
Warning message:
package ‘WCGNA’ is not available (for R version 3.4.3)

[Ram]

Please see my command and compare it to yours. Like I mentioned in my previous comment, you have a typo

[Ram]

Even here, the error happens because you're using library(WCGNA) after installing WGCNA. I thought the typos were being made here on the site and not in your command line, but I guess I was mistaken. Sorry about that!

[prekrish]

Thank you very much for pointing out the typo . I rectified the error and it is now working . I was able to do the analysis without any problem. Thank you so very much for your help and patience :)