Can not install Seurat with install.packages("Seurat")

[JingqunMa]

ERROR: dependency 'png'™ is not available for package 'Seurat'™

• removing ˜'/usr/local/lib/R/site-library/Seurat'€™ Warning in install.packages : installation of package '˜Seurat'€™ had non-zero exit status

[eddelbuettel]

You need to install png first, which may require a libpng-dev package. Please show the errors you get when you try to install png -- in short, no Seurat without png as per the package page too

[JingqunMa]

Thank you @eddelbuettel for the reply. Here is the error when I tried to install png> install.packages("png") Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'https://mran.microsoft.com/snapshot/2019-06-16/src/contrib/png_0.1-7.tar.gz' Content type 'application/octet-stream' length 24990 bytes (24 KB)

downloaded 24 KB

• installing source package ‘png’ ... package ‘png’ successfully unpacked and MD5 sums checked using staged installation ** libs gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include libpng-config --cflags -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o /bin/bash: libpng-config: command not found read.c:3:17: fatal error: png.h: No such file or directory

  include

           ^

  compilation terminated. /usr/local/lib/R/etc/Makeconf:167: recipe for target 'read.o' failed make: *** [read.o] Error 1 ERROR: compilation failed for package ‘png’

• removing ‘/usr/local/lib/R/site-library/png’

The downloaded source packages are in ‘/tmp/Rtmp7kmOsC/downloaded_packages’ Warning message: In install.packages("png") : installation of package ‘png’ had non-zero exit status

[JingqunMa]

libpng-dev also can't be installed. Here is the error: install.packages("libpng-dev") Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning message: package ‘libpng-dev’ is not available (for R version 3.6.0)

[eddelbuettel]

read.c:3:17: fatal error: png.h: No such file or directory #include

You deal with that at the shell command prompt not the R prompt as it is a system library.

[eddelbuettel]

edd@rob:~$ dpkg -S /usr/include/png.h
libpng-dev:amd64: /usr/include/png.h
edd@rob:~$ 

So you need sudo apt-get install libpng-dev to move along.

[JingqunMa]

I am running the docker on a cloud machine which I don't have sudo access.

[eddelbuettel]

You only need sudo inside the container.

If the container does not have the (system-level) png library and headers, then you cannot install the CRAN package png meaning you cannot install CRAN package Seurat. No shortcuts.

You could look into modifying the Docker container and runnning a modified one ...

But in short nothing here is a bug in Rocker so I will close this.

[g-torr]

a workaround for not using sudo is change the PATH and remove temporary the paths pointing to anaconda for the installation, see https://stackoverflow.com/a/59556852 In practise, type in your terminal echo $PATH copy the output on a text editor and remove lines like: /opt/apps/devtools/anaconda/2019.3/python/3.7.3/bin export PATH = 'paste the new path here '

[eddelbuettel]

I suggest we delete this comment. Mixing Rocker with anaconda is a not generally a good idea.