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pachterlab / sleuth

Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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Issue with sleuth install #225

Closed Kappy2 closed 5 years ago

Kappy2 commented 5 years ago

I am trying to install sleuth and seem to run into issues with installing the developer tools. It seems like something is missing. Please help! thanks. I input: biocLite("devtools")

gives the following:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). Installing package(s) ‘devtools’ also installing the dependencies ‘xml2’, ‘roxygen2’, ‘rversions’

trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.2.2.tar.gz' Content type 'application/x-gzip' length 261081 bytes (254 KB)

downloaded 254 KB

trying URL 'https://cloud.r-project.org/src/contrib/roxygen2_6.1.1.tar.gz' Content type 'application/x-gzip' length 178346 bytes (174 KB)

downloaded 174 KB

trying URL 'https://cloud.r-project.org/src/contrib/rversions_2.0.0.tar.gz' Content type 'application/x-gzip' length 9722 bytes

downloaded 9722 bytes

trying URL 'https://cloud.r-project.org/src/contrib/devtools_2.2.0.tar.gz' Content type 'application/x-gzip' length 370794 bytes (362 KB)

downloaded 362 KB

The downloaded source packages are in ‘/tmp/Rtmp1wrGR9/downloaded_packages’ installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, survival Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘xml2’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘roxygen2’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘rversions’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘devtools’ had non-zero exit status

mschilli87 commented 5 years ago

@Kappy2: Which operating system are you on?

The relevant part of the error message is here:

Configuration failed because libxml-2.0 was not found. Try installing:
deb: libxml2-dev (Debian, Ubuntu, etc)
rpm: libxml2-devel (Fedora, CentOS, RHEL)
csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

Did you try to follow these instructions already? If so, where did it fail? If not, please do. :wink:

Kappy2 commented 5 years ago

I'm using atmosphere, on Ubuntu Rstudio. I realized that this file is missing. I poked around on the GUI desktop version to see if I could find the file and I could not. I tried to install the libxml2, but received an error message that the xml2 is not there. I am new to using command line, so I don't know if I am executing those commands correctly.

mschilli87 commented 5 years ago

I don't know about atmosphere but on Ubuntu

sudo apt-get update && \
sudo apt-get install libxml2-dev

should do the trick.

Kappy2 commented 5 years ago

That script gives me an error message. I start R, install biocLite rhdf5, then get stuck..

I am following the directions on this page: https://pachterlab.github.io/sleuth/download

mschilli87 commented 5 years ago

@Kappy2: It would be much easier to help you if you would share the error message you get. Note that the commands I gave you above are not R commands but have to be typed into the command line of your Ubuntu terminal. sleuth requires the R package xml2 which in turn requires the system library libxml-2.0 which on Ubuntu is provided by the software package libxml2-dev. The R error message you copied to your first post told you this much. I told you how to install that package on an Ubuntu system. If you get an error, please share what error at what point. And please try to at least google the error message and solve the problem yourself before asking for help. :wink:

Kappy2 commented 5 years ago

Got it, thank you. Again, complete beginner with command line... learning as I go.

Received another error, tried googling and could not figure it out. I know the error means I have the incorrect path to GitHub, or my access is denied, not sure how to continue from here. Thanks in advance. Input: biocLite("pachterlab/sleuth")

BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15). Installing github package(s) ‘pachterlab/sleuth’ Error: Failed to install 'unknown package' from GitHub: Problem with the SSL CA cert (path? access rights?)

mschilli87 commented 5 years ago

What is the output of

lsb_release

and

dpkg --get-selections | grep curl

(both are Linux commands, not R commands)?

[edit: typo]

Kappy2 commented 5 years ago

Command 'lsb_realease' not found, did you mean:

command 'lsb_release' from deb lsb-release

Try: apt install

and:

curl install libcurl3-gnutls:amd64 install libcurl3-nss:amd64 install libcurl4:amd64 install libcurl4-nss-dev:amd64 install

Kappy2 commented 5 years ago

Sorry, corrected the lab_release : No LSB modules are available.

mschilli87 commented 5 years ago

@Kappy2:

Can you try the following in R?

install.packages("miniCRAN")
install.packages(miniCRAN::pkgDep("devtools"))

This will re-install the devtools package (devtools::install_github is used internally by your biocLite call) and all its dependencies. My guess is there is something off with either you curl and/or httr installation. Also, make sure BiocInstaller::biocValid() returns TRUE on your system.

Kappy2 commented 5 years ago

Could not connect via terminal so couldn't copy and paste correctly, but this is the message I get below: BiocInstaller::biocValid()

error in loadNamespace(name): there is no package called 'bioInstaller'

Kappy2 commented 5 years ago

Just wanted to update you that I got it installed. Cyverse changed something on Ubuntu on their end... Thank you for the help!