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umerijaz / microbiomeSeq

An R package for microbial community analysis in an environmental context
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Failed to install in R 3.6.3 version #45

Open nhdang1998 opened 4 years ago

nhdang1998 commented 4 years ago

Dear author, I really hope that you can update so that microbiomeSeq can be install in R newest version (3.6.3). Thank you.

FilipeMatteoli commented 3 years ago

Hello, microbiomeSeq has several dependencies in Bioconductor. I solved my issues using:

sudo apt-get install r-cran-xml (in terminal) in R: BiocManager::install("impute") BiocManager::install("preprocessCore") BiocManager::install("geneplotter") BiocManager::install("genefilter") BiocManager::install("GO.db") BiocManager::install("DESeq2") install.packages("adespatial")

Then you can: install_github("umerijaz/microbiomeSeq")

AdolfoGrossoGamboa commented 3 years ago

Hello FilipeMatteoli.

In my case, I am working with Rstudio cloud, how could you solve the problem with dependencies? Thanks

AdolfoGrossoGamboa commented 3 years ago

With install_github("umerijaz/microbiomeSeq") I get this error:

trying URL 'http://package-proxy/focal/src/contrib/KMDA_1.0.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://package-proxy/focal/src/contrib/KMDA_1.0.tar.gz' In addition: Warning messages: 1: packages ‘AnnotationDbi’, ‘GO.db’, ‘preprocessCore’, ‘impute’, ‘phyloseq’, ‘DESeq2’ are not available for this version of R

Versions of these packages for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 2: In download.file(url, destfile, method, mode = "wb", ...) : URL 'http://package-proxy/focal/src/contrib/KMDA_1.0.tar.gz': Timeout of 60 seconds was reached Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘KMDA’ failed ERROR: dependencies ‘impute’, ‘preprocessCore’, ‘GO.db’, ‘AnnotationDbi’ are not available for package ‘WGCNA’

The downloaded source packages are in ‘/tmp/RtmpYfE274/downloaded_packages’ ✓ checking for file ‘/tmp/RtmpYfE274/remotesec30a3099e/umerijaz-microbiomeSeq-ffa0090/DESCRIPTION’ ... ─ preparing ‘microbiomeSeq’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘microbiomeSeq_0.1.tar.gz’

Installing package into ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0’ (as ‘lib’ is unspecified) ERROR: dependencies ‘DESeq2’, ‘KMDA’, ‘phyloseq’, ‘WGCNA’ are not available for package ‘microbiomeSeq’

FilipeMatteoli commented 3 years ago

Hi @AdolfoGrossoGamboa, I've never used Rstudio cloud before but whenever I get many package errors like you just showed I prefer to install them stepwise. WGCNA has several dependencies likewise DESeq2, and you may have to manually install dependencies for each one of these packages, Thus taking minor steps will aid to identify the gaps.

As Bioconda moved recently from Bio(c)lite to BiocManager and Microbioseq is 3 years old without updates I believe Bioconda packages fail to be automatically installed.

Regarding the issue "cannot open URL 'http://package-proxy/focal/src/contrib/KMDA_1.0.tar.gz', this may be related to proxy issues has this package download service worked before? If is not reaching the server you can obtain the tar package using wget and manually compile it.