Error : object ‘gaussianff’ is not exported by 'namespace:VGAM'

[xuzhougeng]

I try to install monocle3_alpha as described in http://cole-trapnell-lab.github.io/monocle-release/monocle3/

devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha")

But I come across the following problem

* installing *source* package ‘monocle’ ...
** libs
g++ -std=gnu++11 -I"/home/wangjw/opt/sysoft/lib64/R/include" -DNDEBUG  -I"/home/wangjw/opt/sysoft/lib64/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/wangjw/opt/sysoft/lib64/R/include" -DNDEBUG  -I"/home/wangjw/opt/sysoft/lib64/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -c clustering.cpp -o clustering.o
g++ -std=gnu++11 -I"/home/wangjw/opt/sysoft/lib64/R/include" -DNDEBUG  -I"/home/wangjw/opt/sysoft/lib64/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -c landmark_selection.cpp -o landmark_selection.o
g++ -std=gnu++11 -shared -L/usr/local/lib64 -o monocle.so RcppExports.o clustering.o landmark_selection.o
installing to /home/wangjw/opt/sysoft/lib64/R/library/monocle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Error : object ‘gaussianff’ is not exported by 'namespace:VGAM'
ERROR: lazy loading failed for package ‘monocle’
* removing ‘/home/wangjw/opt/sysoft/lib64/R/library/monocle’
* restoring previous ‘/home/wangjw/opt/sysoft/lib64/R/library/monocle’
Installation failed: Command failed (1)
···

Ths OS of my computer is "CentOS Linux release 7.4.1708 (Core) ", 

And the sessioninfo of my R before installing

```R
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /home/wangjw/opt/sysoft/lib64/R/lib/libRblas.so
LAPACK: /home/wangjw/opt/sysoft/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.0

And after running devtools::install_github, The sessioninfo is

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.0       BiocInstaller_1.30.0 tools_3.5.0         
[4] withr_2.1.2          memoise_1.1.0        git2r_0.23.0        
[7] digest_0.6.15        devtools_1.13.

So does anyone have met the same problem? And how can I fix this problem

[Xiaojieqiu]

Hey @xuzhougeng that seems like an issue resulting from recent changes of VGAM package. The gaussianff is not exported anymore. We will try to fix this issue in our next release soon but for now, could you please try to first install the previous version of VGAM first (VGAM 1.05?) and then install the monocle3 alpha version.
You can download it here and install it manually using install.package function in R :
https://cran.r-project.org/src/contrib/Archive/VGAM/VGAM_1.0-5.tar.gz
(see other archived versions also)

[XiaoliMa]

My system is macOS Sierra 10.12.16. R-version is 3.5.1, when I try to install the the Moncle 3, there some warnings and errors as following.
devtools::install_github("cole-trapnell-lab/L1-graph")

Downloading GitHub repo cole-trapnell-lab/L1-graph@master
from URL https://api.github.com/repos/cole-trapnell-lab/L1-graph/zipball/master
Installing L1Graph
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD
INSTALL
'/private/var/folders/7s/c_q6bx6j6yscv0ft1gktxh_r0000gn/T/Rtmp0jIwsr/devtoolsa7c46d0c49b6/cole-trapnell-lab-L1-graph-c2a3f26'
--library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests

• installing source package ‘L1Graph’ ...
  ** R
  ** tests
  ** byte-compile and prepare package for lazy loading
  Note: possible error in 'principal_graph(X, C0, ': unused arguments (lambda = lambda, gamma = gamma, sigma = sigma)
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
• DONE (L1Graph)

I came to the same problem as above. There is the only VGAM_1.0.6 for mac OS and tried to installed it. There are still lots of errors:

installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
Warning: package ‘DelayedArray’ was built under R version 3.5.1
Error : object ‘gaussianff’ is not exported by 'namespace:VGAM'
ERROR: lazy loading failed for package ‘monocle’

• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle’
  Installation failed: Command failed (1)

[Xiaojieqiu]

@XiaoliMa Please check out the solution I suggested above and let me know how it goes. Thanks

[xuzhougeng]

@Xiaojieqiu According to your suggestion, I download and install VGAM v1.05,

> package.version("VGAM")
[1] "1.0-5

when I try to use devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha") , I found that R will automatically start downloading VGAM_1.0.6 which will cause the problem likes before.

> devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha")
Downloading GitHub repo cole-trapnell-lab/monocle-release@monocle3_alpha
from URL https://api.github.com/repos/cole-trapnell-lab/monocle-release/zipball/monocle3_alpha
Installing monocle
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/VGAM_1.0-6.tar.gz'
Content type 'application/octet-stream' length 2585263 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

Installing VGAM
'/home/wangjw/opt/sysoft/lib64/R/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpivOAd0/devtoolsacaf6e3d4f92/VGAM'  \
  --library='/home/wangjw/opt/sysoft/lib64/R/library' --install-tests 
....
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Error : object ‘gaussianff’ is not exported by 'namespace:VGAM'
ERROR: lazy loading failed for package ‘monocle’

So I clone this repos into local with git clone https://github.com/cole-trapnell-lab/monocle-release.git, then I try install locally with the following commands

cd monocle-release
git checkout monocle3_alpha
cd ..
R CMD INSTALL monocle-release

And the message after I loading this packages is shown below

>library("monocle"
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
> package.version("monocle")
[1] "2.99.1"

Is this means I successfully install monocle3?

[Xiaojieqiu]

@xuzhougeng Definitively, I think you have successfully installed Monocle3. Welcome to the world of Monocle 3!

[XiaoliMa]

I still failed to to install VGAM (1.05 version) on mac version Rstudio. I can only install 1.06 version, which is not right for monocle3.

[Xiaojieqiu]

seems like you don't know how to install VGAM 1.05 locally... please download VGAM 1.05 from the CRAN and install it manually using _

R CMD INSTALL VGAM_1.0-5.tar.gz

in terminal

link to download VGAM 1.05
https://cran.r-project.org/src/contrib/Archive/VGAM/VGAM_1.0-5.tar.gz

[XiaoliMa]

I installed you suggested, the error like this:

install.packages("~/Downloads/VGAM_1.0-5.tar.gz", repos = NULL, type = "source")

• installing source package ‘VGAM’ ...
  ** package ‘VGAM’ successfully unpacked and MD5 sums checked
  ** libs
  clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c VGAM_init.c -o VGAM_init.o
  clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c caqo3.c -o caqo3.o
  gfortran -fPIC -g -O2 -c cqof.f -o cqof.o
  make: gfortran: No such file or directory
  make: *** [cqof.o] Error 1
  ERROR: compilation failed for package ‘VGAM’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/VGAM’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/VGAM’
  Warning in install.packages :
  installation of package ‘/Users/XiaoliMa/Downloads/VGAM_1.0-5.tar.gz’ had non-zero exit status

[Xiaojieqiu]

Hi @XiaoliMa this is an issue related to gfortran based on the error message. You may find this post on the following link helpful:
https://stackoverflow.com/questions/23916219/os-x-package-installation-depends-on-gfortran-4-8

[koenvandenberge]

Hi @Xiaojieqiu , the installation still errors with the older VGAM package you suggested:

> install.packages("~/Downloads/VGAM_1.0-5.tar.gz")
inferring 'repos = NULL' from 'pkgs'
* installing *source* package ‘VGAM’ ...
** package ‘VGAM’ successfully unpacked and MD5 sums checked
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c VGAM_init.c -o VGAM_init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c caqo3.c -o caqo3.o
gfortran   -fPIC  -g -O2  -c cqof.f -o cqof.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
gfortran   -fPIC  -g -O2  -c ei.f -o ei.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
gfortran   -fPIC  -g -O2  -c fgam.f -o fgam.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gautr.c -o gautr.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c lerchphi.c -o lerchphi.o
gfortran   -fPIC  -g -O2  -c lms.f -o lms.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c muxr3.c -o muxr3.o
gfortran   -fPIC  -g -O2  -c rgam.f -o rgam.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rgam3.c -o rgam3.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c specfun3.c -o specfun3.o
gfortran   -fPIC  -g -O2  -c tyeepolygamma.f -o tyeepolygamma.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tyeepolygamma3.c -o tyeepolygamma3.o
gfortran   -fPIC  -g -O2  -c vcall2.f -o vcall2.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
gfortran   -fPIC  -g -O2  -c vdigami.f -o vdigami.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
gfortran   -fPIC  -g -O2  -c veigen.f -o veigen.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
gfortran   -fPIC  -g -O2  -c vgam.f -o vgam.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vgam3.c -o vgam3.o
gfortran   -fPIC  -g -O2  -c vlinpack1.f -o vlinpack1.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
gfortran   -fPIC  -g -O2  -c vlinpack2.f -o vlinpack2.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
gfortran   -fPIC  -g -O2  -c vlinpack3.f -o vlinpack3.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
gfortran   -fPIC  -g -O2  -c vmux.f -o vmux.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vmux3.c -o vmux3.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c zeta3.c -o zeta3.o
clang -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 VGAM.so VGAM_init.o caqo3.o cqof.o ei.o fgam.o gautr.o lerchphi.o lms.o muxr3.o rgam.o rgam3.o specfun3.o tyeepolygamma.o tyeepolygamma3.o vcall2.o vdigami.o veigen.o vgam.o vgam3.o vlinpack1.o vlinpack2.o vlinpack3.o vmux.o vmux3.o zeta3.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/VGAM/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘Rank’ in package ‘VGAM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VGAM)
> devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha")
Downloading GitHub repo cole-trapnell-lab/monocle-release@monocle3_alpha
from URL https://api.github.com/repos/cole-trapnell-lab/monocle-release/zipball/monocle3_alpha
Installing monocle
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/VGAM_1.0-6.tgz'
Content type 'application/x-gzip' length 7852157 bytes (7.5 MB)
==================================================
downloaded 7.5 MB

Installing VGAM
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/ys/t9sslrsd1n3bfwzf3ycl6w740000gn/T/RtmpfVgs7R/devtools79ad78867368/VGAM'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library'  \
  --install-tests 

* installing *binary* package ‘VGAM’ ...
* DONE (VGAM)
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/ys/t9sslrsd1n3bfwzf3ycl6w740000gn/T/RtmpfVgs7R/devtools79ad6f0de255/cole-trapnell-lab-monocle-release-3ff311b'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library'  \
  --install-tests 

* installing *source* package ‘monocle’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -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/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c clustering.cpp -o clustering.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c landmark_selection.cpp -o landmark_selection.o
landmark_selection.cpp:248:7: warning: unused variable 'num_proc' [-Wunused-variable]
  int num_proc = stoi(str_num_proc);
      ^
1 warning generated.
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 monocle.so RcppExports.o clustering.o landmark_selection.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
Warning: package ‘DelayedArray’ was built under R version 3.5.1
Warning: package ‘IRanges’ was built under R version 3.5.1
Error : object ‘gaussianff’ is not exported by 'namespace:VGAM'
ERROR: lazy loading failed for package ‘monocle’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle’
Installation failed: Command failed (1)
> 

[ondp15]

Hello,

I followed the commands from xuzhougeng. When I try the following command local:

R CMD INSTALL monocle-release 
-bash: R: command not found

Overall, this is the code:

source("https://bioconductor.org/biocLite.R")
biocLite("monocle")
devtools::install_github("cole-trapnell-lab/DDRTree", ref="simple-ppt-like")
devtools::install_github("cole-trapnell-lab/L1-graph")
install.packages("reticulate")
library(reticulate)
py_install('umap-learn', pip = T, pip_ignore_installed = T) # Ensure the latest version of UMAP is installed
py_install("louvain")
#Manually install VGAM1.0-5
package.version("VGAM")
devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha")
# use local terminal 
# git clone https://github.com/cole-trapnell-lab/monocle-release.git
# cd monocle-release
# git checkout monocle3_alpha
# cd ..
# R CMD INSTALL monocle-release 
# But my R CMD INSTALL does not work on local terminal 
install.packages("/Users/onarvaez/monocle-release")
# says package ‘/Users/onarvaez/monocle-release’ is not available (for R version 3.5.1) 
library(monocle)

Part of the output:

package.version("VGAM")
[1] "1.0-5"
> devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha")
Downloading GitHub repo cole-trapnell-lab/monocle-release@monocle3_alpha
from URL https://api.github.com/repos/cole-trapnell-lab/monocle-release/zipball/monocle3_alpha
Installing monocle
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/VGAM_1.0-6.tgz'
Content type 'application/x-gzip' length 7852157 bytes (7.5 MB)
==================================================
downloaded 7.5 MB

Installing VGAM
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/jh/wvznsryx3g7b9bkr9p1krqg063lgyq/T/RtmpPV02Xn/devtools415b1f73726c/VGAM'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests 

* installing *binary* package ‘VGAM’ ...
* DONE (VGAM)
Reloading installed VGAM
Installation failed: Namespace not found for VGAM. Is it loaded?
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/jh/wvznsryx3g7b9bkr9p1krqg063lgyq/T/RtmpPV02Xn/devtools415b6bb0a285/cole-trapnell-lab-monocle-release-3ff311b'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests 

* installing *source* package ‘monocle’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -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/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c clustering.cpp -o clustering.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c landmark_selection.cpp -o landmark_selection.o
landmark_selection.cpp:248:7: warning: unused variable 'num_proc' [-Wunused-variable]
  int num_proc = stoi(str_num_proc);
      ^
1 warning generated.
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 monocle.so RcppExports.o clustering.o landmark_selection.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
Error : object ‘gaussianff’ is not exported by 'namespace:VGAM'
ERROR: lazy loading failed for package ‘monocle’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle’
Installation failed: Command failed (1)

Thanks,

Ode

[romanhaa]

Yep, you can install an older VGAM version manually but during the monocle3 installing process it will be updated. I have the same issue as the previous posters.

[zbgaber]

I was having romanhaa's problem too. I would manually reinstall VGAM 1.05 but when I installed monocle3, VGAM would update to 1.06. I found that you could get around this using the argument dep = FALSE (tells devtools not to automatically update dependencies).

I also added argument force = TRUE, but I'm not sure if that's necessary.

Anyways, after manually uploading VGAM 1.05 in console, using this code got me able to install monocle3:

devtools::install_github("cole-trapnell-lab/monocle-release", ref = "monocle3_alpha", force = TRUE, dep = FALSE)

[gexijin]

I also had a lot of trouble installing monocle 3. But eventually, I made it work. Here is summary of what I did, partially based on the info above and other posts.

1. Install an older version of VGAM.
   remove.packages("VGAM") # remove the 1.0-6
   download.files("https://cran.r-project.org/src/contrib/Archive/VGAM/VGAM_1.0-5.tar.gz",
   "VGAM_1.0-5.tar.gz")
   install.packages(""VGAM_1.0-5.tar.gz", repos = NULL, type = "source")

2. Install Rtools software in Windows. https://cran.r-project.org/bin/windows/Rtools/
   I don't know why, but even though a version of Rtools is installed under R3.5.1 folder. The path is messed up, as the compiler of monocle 3 tries to run C:\Rtools....

3. Close Rstudio and moved to R itself, which uses C:\Rtools. Rtools 3.5 does not work with R 3.5.1. Solve this with instructions from this page: find_rtools() doesn't recognize Rtools 3.5 in R 3.5.0 r-lib/devtools#1772

library(devtools)
assignInNamespace("version_info", c(devtools:::version_info, list("3.5" = list(version_min = "3.3.0", version_max = "99.99.99", path = "bin"))), "devtools")
find_rtools() # is TRUE now
devtools::install_github("r-lib/devtools")

4. Install monocle 3 from R (not Rstudio).
   devtools::install_github("cole-trapnell-lab/monocle-release", ref = "monocle3_alpha", force = TRUE, dep = FALSE)

Worked for me.

[ciuhkimo]

@Xiaojieqiu , I tried to installed the 1.0-5 version, but I cannot install it. It showed that
In R CMD INSTALL

• installing source package 'VGAM' ...
  ** package 'VGAM' successfully unpacked and MD5 sums checked
  ** libs

*** arch - i386
Warning in system(cmd) : 'make' not found
ERROR: compilation failed for package 'VGAM'

• removing 'C:/Program Files/R/R-3.5.1/library/VGAM'
• restoring previous 'C:/Program Files/R/R-3.5.1/library/VGAM'
  Warning message:
  In install.packages("~/Downloads/VGAM_1.0-5.tar.gz", repos = NULL, :
  installation of package 'C:/Users/u1/Documents/Downloads/VGAM_1.0-5.tar.
  gz' had non-zero exit status

[romanhaa]

@ciuhkimo You could start by looking up that error on Google and will find that the make command belongs the compiler libraries that you seem to be missing on your computer.

[liu2005678]

Try the following lines:
library(remotes) # if "remotes" not installed, then install.packages("remotes") first
install_version("VGAM", version="1.0-5")
library(VGAM)