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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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Error when installing Tax4Fun #490

Closed emankhalaf closed 6 years ago

emankhalaf commented 6 years ago

Hi,

I try to download Tax4Fun package using its readme doc. I use R CMD INSTALL Tax4Fun_0.3.1.tar.gz

Then I got this error:

So, I installed qiimer, (biomformat is already installed), then I repeated the command but still get the same error.

Swift help is much appreciated. Thanks Eman

benjjneb commented 6 years ago

Did you install qiimer and biom packages in that conda environment? I.e. if you open an R session in that conda environment, can you load those packages? Also, biom would be a different package than biomformat.

Other than that, you might have to ask the Tax4Fun people for help, I haven't actually used that package.

emankhalaf commented 6 years ago

I repeated installation from R console, but this time the error include biom package. I have biomformat as Biom has been deprecated. I will try to contact people of Tax4Fun. Thanks

emankhalaf commented 6 years ago

Yes, it is solved. Create a conda environment, then install Tax4Fun and its dependencies in it. You can install biom packge (deprecated) in the environment. Then you can see the package installed in Rstudio, ready for loading. Let me know if it works or not. Good luck

shandas29 commented 6 years ago

Hello Emankhalaf, I am also having the same problem in Installing Tax4Fun. Can you please guide me on how to successfully install Tax4Fun in R?

ylock commented 4 years ago

hi ,I have salve this problem by installed with source code,like this: download the qiimer and biom source code qiimer : (https://cran.r-project.org/src/contrib/Archive/qiimer/) biom : (https://cran.r-project.org/src/contrib/Archive/biom/),for this two R packages you need to install tow dependence (pheatmap)(RJSONIO),and then you can install Tax4Fun. log like this :

install.packages("qiimer_0.9.4.tar.gz") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) inferring 'repos = NULL' from 'pkgs' ERROR: dependency 'pheatmap' is not available for package 'qiimer'

  • removing '/usr/local/lib/R/site-library/qiimer' Warning message: In install.packages("qiimer_0.9.4.tar.gz") : installation of package 'qiimer_0.9.4.tar.gz' had non-zero exit status install.packages("pheatmap") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) ^[[Ctrying URL 'https://cloud.r-project.org/src/contrib/pheatmap_1.0.12.tar.gz' Content type 'application/x-gzip' length 15071 bytes (14 KB)

    downloaded 14 KB

The downloaded source packages are in '/tmp/RtmpUhX232/downloaded_packages'

install.packages("qiimer_0.9.4.tar.gz") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) inferring 'repos = NULL' from 'pkgs'

  • installing source package 'qiimer' ... package 'qiimer' successfully unpacked and MD5 sums checked using staged installation R data inst byte-compile and prepare package for lazy loading ** help * installing help indices building package indices testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path

  • DONE (qiimer)

    install.packages("biom_0.3.12.tar.gz") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) inferring 'repos = NULL' from 'pkgs' ERROR: dependency 'RJSONIO' is not available for package 'biom'

  • removing '/usr/local/lib/R/site-library/biom' Warning message: In install.packages("biom_0.3.12.tar.gz") : installation of package 'biom_0.3.12.tar.gz' had non-zero exit status install.packages("RJSONIO") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/RJSONIO_1.3-1.4.tar.gz' Content type 'application/x-gzip' length 1166882 bytes (1.1 MB)

    downloaded 1.1 MB

The downloaded source packages are in '/tmp/RtmpSngcef/downloaded_packages'

install.packages("biom_0.3.12.tar.gz") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) inferring 'repos = NULL' from 'pkgs'

  • installing source package 'biom' ... package 'biom' successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading Creating a generic function for 'nrow' from package 'base' in package 'biom' Creating a generic function for 'ncol' from package 'base' in package 'biom' Creating a generic function for 'rownames' from package 'base' in package 'biom' Creating a generic function for 'colnames' from package 'base' in package 'biom' help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path

  • DONE (biom)

    install.packages("Tax4Fun_0.3.1.tar.gz" ,repos = NULL, type = "source") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified)

  • installing source package 'Tax4Fun' ... using staged installation R data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading * help installing help indices building package indices testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path
  • DONE (Tax4Fun)

well ,hope to help you .

FilipeMatteoli commented 3 years ago

This is much easier now using https://rdrr.io/github/nick-youngblut/Tax4Fun/. qiimer still has to be installed from source though.