Error installing velocyto.R

[wen-zhou-caltech]

Anyone can help me with these errors?

ERROR: dependencies ‘pcaMethods’, ‘h5’ are not available for package ‘velocyto.R’

Thanks!

[pkharchenko]

Please install pcaMethods and h5 packages. Also, are you using the latest version (on github)? These packages should have been added during the installation procedure as they’re specified in the Imports section. Best, -peter.

…

On Jun 15, 2018, at 16:11, cynthiazhou1005 ***@***.***> wrote: Anyone can help me with these errors? ERROR: dependencies ‘pcaMethods’, ‘h5’ are not available for package ‘velocyto.R’ Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[wen-zhou-caltech]

I tried in the docker system but keeps getting this error:

Build an image from a Dockerfile
dhcp-35-214:debian9 wenzhou$ docker build -t velocyto .
Sending build context to Docker daemon 3.072kB
Step 1/12 : FROM rocker/r-ver:3.4
---> 0e2de7cecea5
Step 2/12 : MAINTAINER Peter Kharchenko "peter_kharchenko@hms.harvard.edu"
---> Using cache
---> b82b68baba4e
Step 3/12 : RUN apt-get update --yes && apt-get install --no-install-recommends --yes build-essential cmake git libbamtools-dev libboost-dev libboost-iostreams-dev libboost-log-dev libboost-system-dev libboost-test-dev libssl-dev libcurl4-openssl-dev libz-dev curl libhdf5-cpp-100 libarmadillo7 libarmadillo-dev
---> Using cache
---> e5076dc51334
Step 4/12 : RUN R -e 'chooseCRANmirror(ind=52); install.packages(c("devtools", "Rcpp","RcppArmadillo", "Matrix", "mgcv", "abind","igraph","h5","Rtsne","cluster","data.table"))'
---> Using cache
---> c7f5a37ff12a
Step 5/12 : RUN R -e 'source("https://bioconductor.org/biocLite.R"); biocLite(c("pcaMethods","edgeR","Rsamtools","GenomicAlignments","GenomeInfoDb","Biostrings"),suppressAutoUpdate=TRUE,ask=FALSE,suppressUpdates=TRUE)'
---> Using cache
---> 7ce78f9e51a7
Step 6/12 : RUN useradd -m user
---> Using cache
---> 97ad247e7cc7
Step 7/12 : USER user
---> Using cache
---> 40500956bb83
Step 8/12 : ENTRYPOINT ["/bin/bash"]
---> Using cache
---> e3dabf4d15fb
Step 9/12 : WORKDIR "/home/user"
---> Using cache
---> d7855a53b679
Step 10/12 : RUN git clone https://github.com/velocyto-team/velocyto.R && mkdir -p /R/x86_64-redhat-linux-gnu-library/3.4
---> Using cache
---> 939a53920a1c
Step 11/12 : RUN echo '.libPaths(c("/R/x86_64-redhat-linux-gnu-library/3.4", .libPaths()))' > .Rprofile && R -e 'devtools::install_local("~/velocyto.R/",dep=T,upgrade_dependencies=F)'
---> Running in 5bf5af47e104

R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

devtools::install_local("/velocyto.R/",dep=T,upgrade_dependencies=F)
Error in loadNamespace(name) : there is no package called ‘devtools’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne ->
Execution halted
The command '/bin/sh -c echo '.libPaths(c("/R/x86_64-redhat-linux-gnu-library/3.4", .libPaths()))' > .Rprofile && R -e 'devtools::install_local("~/velocyto.R/",dep=T,upgrade_dependencies=F)'' returned a non-zero code: 1

Any advice please? Thank you!

[alexbarrera]

@pkharchenko @cynthiazhou1005 I suspect this might be the same problem I'm having, which has also been reproduced by @vagnec here as an issue with h5.

The problem seems to boil down to the installation of h5, now deprecated. Is there any known solution to this problem?

Is there any plan to update the dependency to the new hdf5r package? This has already been asked in #42, but I want to reflect that at least in my case, the request would be motivated by the issues installing velocyto.R with the current h5 package as a dependency.

Thanks!

[pkharchenko]

It should be quite straightforward to switch to hdf5r … unfortunately I’d be able to get to it in next couple of weeks ... if someone can test/submit patch, I’ll gladly accept it. It’s used in only two functions: read.loom.matrices() and read.gene.mapping.info().

…

On Oct 15, 2018, at 11:59 AM, Alejandro Barrera ***@***.***> wrote: @pkharchenko <https://github.com/pkharchenko> @cynthiazhou1005 <https://github.com/cynthiazhou1005> I suspect this might be the same problem I'm having, which has also been reproduced by @vagnec <https://github.com/vagnec> here <mannau/h5#72> as an issue with h5. The problem seems to boil down to the installation of h5, now deprecated. Is there any known solution to this problem? Is there any plan to update the dependency to the new hdf5r package? This has already been asked in #42 <#42>, but I want to reflect that at least in my case, the request would be motivated by the issues installing velocyto.R with the current h5 package as a dependency. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#30 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALT78t4f-sZWkJLvDJA2r-hRK_lEnS-5ks5ulLD3gaJpZM4UqFyz>.

[Puriney]

Since my issue happened to be No. 42, I felt 'obligated' to make it happen. 😄 The PR (#43) hopefully works.

[Shians]

pcaMethods is a Bioconductor dependency, which install_github() will not automatically pick up on. You can get around this by adding something like biocViews: Software to your DESCRIPTION, to make install_github() think you're a Bioconductor package and be able to install the dependency correctly.

[brianpenghe]

I tried in the docker system but keeps getting this error:

Build an image from a Dockerfile
dhcp-35-214:debian9 wenzhou$ docker build -t velocyto .
Sending build context to Docker daemon 3.072kB
Step 1/12 : FROM rocker/r-ver:3.4
---> 0e2de7cecea5
Step 2/12 : MAINTAINER Peter Kharchenko "peter_kharchenko@hms.harvard.edu"
---> Using cache
---> b82b68baba4e
Step 3/12 : RUN apt-get update --yes && apt-get install --no-install-recommends --yes build-essential cmake git libbamtools-dev libboost-dev libboost-iostreams-dev libboost-log-dev libboost-system-dev libboost-test-dev libssl-dev libcurl4-openssl-dev libz-dev curl libhdf5-cpp-100 libarmadillo7 libarmadillo-dev
---> Using cache
---> e5076dc51334
Step 4/12 : RUN R -e 'chooseCRANmirror(ind=52); install.packages(c("devtools", "Rcpp","RcppArmadillo", "Matrix", "mgcv", "abind","igraph","h5","Rtsne","cluster","data.table"))'
---> Using cache
---> c7f5a37ff12a
Step 5/12 : RUN R -e 'source("https://bioconductor.org/biocLite.R"); biocLite(c("pcaMethods","edgeR","Rsamtools","GenomicAlignments","GenomeInfoDb","Biostrings"),suppressAutoUpdate=TRUE,ask=FALSE,suppressUpdates=TRUE)'
---> Using cache
---> 7ce78f9e51a7
Step 6/12 : RUN useradd -m user
---> Using cache
---> 97ad247e7cc7
Step 7/12 : USER user
---> Using cache
---> 40500956bb83
Step 8/12 : ENTRYPOINT ["/bin/bash"]
---> Using cache
---> e3dabf4d15fb
Step 9/12 : WORKDIR "/home/user"
---> Using cache
---> d7855a53b679
Step 10/12 : RUN git clone https://github.com/velocyto-team/velocyto.R && mkdir -p /R/x86_64-redhat-linux-gnu-library/3.4
---> Using cache
---> 939a53920a1c
Step 11/12 : RUN echo '.libPaths(c("/R/x86_64-redhat-linux-gnu-library/3.4", .libPaths()))' > .Rprofile && R -e 'devtools::install_local("~/velocyto.R/",dep=T,upgrade_dependencies=F)'
---> Running in 5bf5af47e104

R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

devtools::install_local("/velocyto.R/",dep=T,upgrade_dependencies=F)
Error in loadNamespace(name) : there is no package called ‘devtools’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne ->
Execution halted
The command '/bin/sh -c echo '.libPaths(c("/R/x86_64-redhat-linux-gnu-library/3.4", .libPaths()))' > .Rprofile && R -e 'devtools::install_local("~/velocyto.R/",dep=T,upgrade_dependencies=F)'' returned a non-zero code: 1

Any advice please? Thank you!

Does this work:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pcaMethods", version = "3.8")