Installation failing

[Connorr0]

I am trying to install Signac on a new Mac and am unclear on what is going wrong.

> setRepositories(ind=1:2)
> install.packages("Signac")
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘Signac’
Do you want to attempt to install these from sources? (Yes/no/cancel) y
installing the source package ‘Signac’

trying URL 'https://cran.rstudio.com/src/contrib/Signac_1.0.0.tar.gz'
Content type 'application/x-gzip' length 702895 bytes (686 KB)
==================================================
downloaded 686 KB

* installing *source* package ‘Signac’ ...
** package ‘Signac’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c filter.cpp -o filter.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c group.cpp -o group.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c validate.cpp -o validate.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Signac.so RcppExports.o filter.o group.o validate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Signac/00new/Signac/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
sh: line 1:  7055 Killed: 9               R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --slave 2>&1 < '/var/folders/s6/sgdnr_3x3311v4jn8581ns9h0000gn/T//RtmpjPE12q/file1b7c7673880e'
ERROR: lazy loading failed for package ‘Signac’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Signac’
Warning in install.packages :
  installation of package ‘Signac’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/s6/sgdnr_3x3311v4jn8581ns9h0000gn/T/RtmpC7Xhf3/downloaded_packages’

[timoast]

I was able to install Signac on macOS Catalina R 4.0.2 without any issues. Did you install Bioconductor first?

[Connorr0]

Yes, although this computer was still using R 3.6

[timoast]

Killed: 9 is usually due to running out of RAM but I don't know why this would happen during installation (unless you had a tiny amount of RAM available). You could try restarting R and installing again in a fresh R session, and if that doesn't work maybe install R 4.0.2

[timoast]

If you're in a rush to get this working you could also use the docker image

[alutservitz]

Hi Tim,
I am getting the same error when installing Signac. I am using macOS Catalina, R 4.0.2, have enough RAM, and have Bioconductor version 3.11. Any idea on what my issue may be?

[timoast]

@lutservitz try installing in a fresh R session (outside of RStudio)

[alutservitz]

@timoast Hi Tim, thanks for your reply! I receive the same error in a fresh R session outside of RStudio as well.

I just ran again, and here is the error I receive:

`installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Signac/00new/Signac/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 23740 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/xr/4zs5t6756l75s3p43j5j6qj40000gn/T//Rtmpdg8PZQ/file5ca92a247767'
ERROR: lazy loading failed for package ‘Signac’

• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Signac’

The downloaded source packages are in
‘/private/var/folders/xr/4zs5t6756l75s3p43j5j6qj40000gn/T/RtmpOn3IYD/downloaded_packages’
Warning message:
In install.packages("Signac") :
installation of package ‘Signac’ had non-zero exit status`

[timoast]

Try reinstalling Rcpp (install.packages("Rcpp"))

If that still doesn't work you could try the suggestions here: satijalab/seurat#3273 (comment)

[YiminZhao97]

Hi, everyone. I got a similar question. I am using R 4.0.2 in Mac. When I want to install Signac, it failed. The errors are like that.

The downloaded source packages are in
‘/private/var/folders/xj/m5zq_92n51582531fb0hz3tm0000gn/T/RtmpCsTMcK/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘lmtest’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘stringi’ had non-zero exit status

[timoast]

@YiminZhao97 you need to install those packages that failed (install.packages(c("stringi", "lmtest")))

[YiminZhao97]

@TimoAS Hi, Tim. I did just like you suggested.
install.packages(c("stringi", "lmtest"))

There are binary versions available but the source versions are later:
binary source needs_compilation
stringi 1.4.6 1.5.3 TRUE
lmtest 0.9-37 0.9-38 TRUE

Do you want to install from sources the packages which need compilation? (Yes/no/cancel)

I chose Yes. Then it failed like this:
Error in download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb"): download from 'http://www.gagolewski.com/software/stringi/icudt61l.zip' failed

icudt download failed
Error: Stopping on error
In addition: Warning messages:
1: In download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb") :
URL 'https://raw.githubusercontent.com/gagolews/stringi/master/src/icu61/data/icudt61l.zip': status was 'Couldn't connect to server'
2: In download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb") :
URL 'https://raw.githubusercontent.com/gagolews/stringi/master/src/icu55/data/icudt61l.zip': status was 'Couldn't connect to server'
: In download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb") :
URL 'http://raw.githubusercontent.com/gagolews/stringi/master/src/icu61/data/icudt61l.zip': status was 'Couldn't connect to server'
4: In download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb") :
URL 'http://raw.githubusercontent.com/gagolews/stringi/master/src/icu55/data/icudt61l.zip': status was 'Couldn't connect to server'
5: In download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb") :
downloaded length 84647 != reported length 10791080
6: In download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb") :
URL 'http://www.ibspan.waw.pl/~gagolews/stringi/icudt61l.zip': status was 'Failure when receiving data from the peer'
7: In download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb") :
downloaded length 2084855 != reported length 10791080
8: In download.file(paste(href, fname, sep = ""), icudtzipfname, mode = "wb") :
URL 'http://www.gagolewski.com/software/stringi/icudt61l.zip': status was 'Transferred a partial file'
Execution halted
*** icudt download failed. stopping.
ERROR: configuration failed for package ‘stringi’

• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/stringi’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/stringi’
  Warning in install.packages :
  installation of package ‘stringi’ had non-zero exit status
• installing source package ‘lmtest’ ...
  ** 成功将‘lmtest’程序包解包并MD5和检查
  ** using staged installation
  ** libs
  clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
  gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c pan.f -o pan.o
  make: gfortran: No such file or directory
  make: *** [pan.o] Error 1
  ERROR: compilation failed for package ‘lmtest’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/lmtest’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/lmtest’
  Warning in install.packages :
  installation of package ‘lmtest’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/xj/m5zq_92n51582531fb0hz3tm0000gn/T/RtmpCsTMcK/downloaded_packages’

[timoast]

@YiminZhao97 you can choose "No" to install the pre-compiled binaries rather than compiling from source

[YiminZhao97]

@timoast Thank you very much! And I have successfully installed Seurat. One further question, I also want to install Signac. But it shows that I did't install gggenes. So I install it but it gives my errors like this, what should I do?
install.packages('gggenes')
also installing the dependencies ‘shades’, ‘ggfittext’

试开URL’https://cran.rstudio.com/bin/macosx/contrib/4.0/shades_1.4.0.tgz'
Content type 'application/x-gzip' length 86119 bytes (84 KB)

downloaded 84 KB

试开URL’https://cran.rstudio.com/bin/macosx/contrib/4.0/ggfittext_0.9.0.tgz'
Content type 'application/x-gzip' length 688487 bytes (672 KB)

downloaded 415 KB

Warning in install.packages :
downloaded length 425080 != reported length 688487
Warning in install.packages :
URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/ggfittext_0.9.0.tgz': status was 'Failure when receiving data from the peer'
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://cran.rstudio.com/bin/macosx/contrib/4.0/ggfittext_0.9.0.tgz' failed
Warning in install.packages :
download of package ‘ggfittext’ failed
试开URL’https://cran.rstudio.com/bin/macosx/contrib/4.0/gggenes_0.4.0.tgz'
Content type 'application/x-gzip' length 1264076 bytes (1.2 MB)

downloaded 896 KB

Warning in install.packages :
downloaded length 917720 != reported length 1264076
Warning in install.packages :
URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/gggenes_0.4.0.tgz': status was 'Failure when receiving data from the peer'
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://cran.rstudio.com/bin/macosx/contrib/4.0/gggenes_0.4.0.tgz' failed
Warning in install.packages :
download of package ‘gggenes’ failed

The downloaded binary packages are in
/var/folders/xj/m5zq_92n51582531fb0hz3tm0000gn/T//RtmpCsTMcK/downloaded_packages

[timoast]

It looks like you're having issues downloading from CRAN, probably due to internet connectivity issues. You'll have to fix your internet connection