Error on instaling progject dependencies

LanaZet commented 3 years ago

Hey! im stucked at the moment of installing Phyloscanner dependency. Can you help me please?


user@BDI-pathogens-VirtualBox:~/phyloscanner$ cd phyloscannerR/
user@BDI-pathogens-VirtualBox:~/phyloscanner/phyloscannerR$ sudo R
[sudo] password for user: 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

  Natural language support but running in an English locale

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.

> install('.', dependencies = T)
Error in install(".", dependencies = T) : 
  could not find function "install"
> library(devtools)
> install('.', dependencies = T)
Installing phyloscannerR
trying URL 'https://cran.rstudio.com/src/contrib/network_1.17.1.tar.gz'
Content type 'application/x-gzip' length 511920 bytes (499 KB)
==================================================
downloaded 499 KB

Installing network
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e7abaf695/network'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘network’ ...
** package ‘network’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c access.c -o access.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c constructors.c -o constructors.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c layout.c -o layout.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o network.so Rinit.o access.o constructors.o layout.o utils.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/network/libs
** R
** data
** inst
** tests
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘statnet.common’ 4.0.0 is being loaded, but >= 4.5 is required
ERROR: lazy loading failed for package ‘network’
* removing ‘/usr/local/lib/R/site-library/network’
* restoring previous ‘/usr/local/lib/R/site-library/network’
Installation failed: Command failed (1)
trying URL 'https://cloud.r-project.org/src/contrib/prodlim_2019.11.13.tar.gz'
Content type 'application/x-gzip' length 126048 bytes (123 KB)
==================================================
downloaded 123 KB

Installing prodlim
trying URL 'https://cloud.r-project.org/src/contrib/lava_1.6.10.tar.gz'
Content type 'application/x-gzip' length 1631414 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

Installing lava
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e7326ceccd/lava'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

ERROR: dependency ‘progressr’ is not available for package ‘lava’
* removing ‘/usr/local/lib/R/site-library/lava’
Installation failed: Command failed (1)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e745dc4e0f/prodlim'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

ERROR: dependency ‘lava’ is not available for package ‘prodlim’
* removing ‘/usr/local/lib/R/site-library/prodlim’
Installation failed: Command failed (1)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/home/user/phyloscanner/phyloscannerR'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

ERROR: dependency ‘prodlim’ is not available for package ‘phyloscannerR’
* removing ‘/usr/local/lib/R/site-library/phyloscannerR’
user@BDI-pathogens-VirtualBox:~$ cd phyloscanner/
user@BDI-pathogens-VirtualBox:~/phyloscanner$ cd phyloscannerR/
user@BDI-pathogens-VirtualBox:~/phyloscanner/phyloscannerR$ sudo R
[sudo] password for user: 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

  Natural language support but running in an English locale

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.

> install('.', dependencies = T)
Error in install(".", dependencies = T) : 
  could not find function "install"
> library(devtools)
> install('.', dependencies = T)
Installing phyloscannerR
trying URL 'https://cran.rstudio.com/src/contrib/network_1.17.1.tar.gz'
Content type 'application/x-gzip' length 511920 bytes (499 KB)
==================================================
downloaded 499 KB

Installing network
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e7abaf695/network'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘network’ ...
** package ‘network’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c access.c -o access.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c constructors.c -o constructors.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c layout.c -o layout.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o network.so Rinit.o access.o constructors.o layout.o utils.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/network/libs
** R
** data
** inst
** tests
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘statnet.common’ 4.0.0 is being loaded, but >= 4.5 is required
ERROR: lazy loading failed for package ‘network’
* removing ‘/usr/local/lib/R/site-library/network’
* restoring previous ‘/usr/local/lib/R/site-library/network’
Installation failed: Command failed (1)
trying URL 'https://cloud.r-project.org/src/contrib/prodlim_2019.11.13.tar.gz'
Content type 'application/x-gzip' length 126048 bytes (123 KB)
==================================================
downloaded 123 KB

Installing prodlim
trying URL 'https://cloud.r-project.org/src/contrib/lava_1.6.10.tar.gz'
Content type 'application/x-gzip' length 1631414 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

Installing lava
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e7326ceccd/lava'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

ERROR: dependency ‘progressr’ is not available for package ‘lava’
* removing ‘/usr/local/lib/R/site-library/lava’
Installation failed: Command failed (1)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e745dc4e0f/prodlim'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

ERROR: dependency ‘lava’ is not available for package ‘prodlim’
* removing ‘/usr/local/lib/R/site-library/prodlim’
Installation failed: Command failed (1)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/home/user/phyloscanner/phyloscannerR'  \
  --library='/usr/local/lib/R/site-library' --install-tests 
ERROR: dependency ‘prodlim’ is not available for package ‘phyloscannerR’
* removing ‘/usr/local/lib/R/site-library/phyloscannerR’
user@BDI-pathogens-VirtualBox:~$ cd phyloscanner/
user@BDI-pathogens-VirtualBox:~/phyloscanner$ cd phyloscannerR/
user@BDI-pathogens-VirtualBox:~/phyloscanner/phyloscannerR$ sudo R
[sudo] password for user: 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

  Natural language support but running in an English locale

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.

> install('.', dependencies = T)
Error in install(".", dependencies = T) : 
  could not find function "install"
> library(devtools)
> install('.', dependencies = T)
Installing phyloscannerR
trying URL 'https://cran.rstudio.com/src/contrib/network_1.17.1.tar.gz'
Content type 'application/x-gzip' length 511920 bytes (499 KB)
==================================================
downloaded 499 KB

Installing network
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e7abaf695/network'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘network’ ...
** package ‘network’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c access.c -o access.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c constructors.c -o constructors.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c layout.c -o layout.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o network.so Rinit.o access.o constructors.o layout.o utils.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/network/libs
** R
** data
** inst
** tests
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘statnet.common’ 4.0.0 is being loaded, but >= 4.5 is required
ERROR: lazy loading failed for package ‘network’
* removing ‘/usr/local/lib/R/site-library/network’
* restoring previous ‘/usr/local/lib/R/site-library/network’
Installation failed: Command failed (1)
trying URL 'https://cloud.r-project.org/src/contrib/prodlim_2019.11.13.tar.gz'
Content type 'application/x-gzip' length 126048 bytes (123 KB)
==================================================
downloaded 123 KB

Installing prodlim
trying URL 'https://cloud.r-project.org/src/contrib/lava_1.6.10.tar.gz'
Content type 'application/x-gzip' length 1631414 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

Installing lava
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e7326ceccd/lava'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

ERROR: dependency ‘progressr’ is not available for package ‘lava’
* removing ‘/usr/local/lib/R/site-library/lava’
Installation failed: Command failed (1)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpeRoc5x/devtools6e745dc4e0f/prodlim'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

ERROR: dependency ‘lava’ is not available for package ‘prodlim’
* removing ‘/usr/local/lib/R/site-library/prodlim’
Installation failed: Command failed (1)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/home/user/phyloscanner/phyloscannerR'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

ERROR: dependency ‘prodlim’ is not available for package ‘phyloscannerR’
* removing ‘/usr/local/lib/R/site-library/phyloscannerR’
Erro```### ``

mdhall272 commented 3 years ago

Please try upgrading to R 4 and trying again? I've now changed the phyloscannerR DESCRIPTION to require 4.0.0, since there are significant issues with ggtree and older versions.

LanaZet commented 2 years ago

I have done this, now i see this error:

 install('.', dependencies = T)
Skipping 2 packages not available: treeio, ggtree
Installing 4 packages: vroom, readr, haven, tidyverse
Installing packages into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/vroom_1.5.6.tar.gz'
Content type 'application/x-gzip' length 727855 bytes (710 KB)
==================================================
downloaded 710 KB

trying URL 'https://cloud.r-project.org/src/contrib/readr_2.1.0.tar.gz'
Content type 'application/x-gzip' length 519991 bytes (507 KB)
==================================================
downloaded 507 KB

trying URL 'https://cloud.r-project.org/src/contrib/haven_2.4.3.tar.gz'
Content type 'application/x-gzip' length 296805 bytes (289 KB)
==================================================
downloaded 289 KB

trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.1.tar.gz'
Content type 'application/x-gzip' length 702779 bytes (686 KB)
==================================================
downloaded 686 KB

ERROR: failed to lock directory ‘/usr/local/lib/R/site-library’ for modifying
Try removing ‘/usr/local/lib/R/site-library/00LOCK-vroom’
ERROR: dependency ‘vroom’ is not available for package ‘readr’
* removing ‘/usr/local/lib/R/site-library/readr’
ERROR: dependency ‘readr’ is not available for package ‘haven’
* removing ‘/usr/local/lib/R/site-library/haven’
ERROR: dependencies ‘haven’, ‘readr’ are not available for package ‘tidyverse’
* removing ‘/usr/local/lib/R/site-library/tidyverse’

The downloaded source packages are in
    ‘/tmp/RtmpVLnEvb/downloaded_packages’
✔  checking for file ‘/home/user/phyloscanner/phyloscannerR/DESCRIPTION’
─  preparing ‘phyloscannerR’:
✔  checking DESCRIPTION meta-information ... OK
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘phyloscannerR_1.8.0.tar.gz’

Running /usr/lib/R/bin/R CMD INSTALL \
  /tmp/RtmpVLnEvb/phyloscannerR_1.8.0.tar.gz --install-tests 
* installing to library ‘/usr/local/lib/R/site-library’
ERROR: dependency ‘tidyverse’ is not available for package ‘phyloscannerR’
* removing ‘/usr/local/lib/R/site-library/phyloscannerR’
Error in (function (command = NULL, args = character(), error_on_status = TRUE,  : 
  System command 'R' failed, exit status: 1, stdout & stderr were printed
Type .Last.error.trace to see where the error occurred
In addition: Warning messages:
1: In i.p(...) : installation of package ‘vroom’ had non-zero exit status
2: In i.p(...) : installation of package ‘readr’ had non-zero exit status
3: In i.p(...) : installation of package ‘haven’ had non-zero exit status
4: In i.p(...) :
  installation of package ‘tidyverse’ had non-zero exit status

Didn't have access to edit folder

mdhall272 commented 2 years ago

I don't know - the error occurs before it even tries to install phyloscanner. Try reinstalling the tidyverse? Upgrading to R 4 means you basically have to reinstall everything, unfortunately.

LanaZet commented 2 years ago

i think the problem in blocked folder, programm has no access to it.

mdhall272 commented 2 years ago

Try this? https://stackoverflow.com/questions/14382209/r-install-packages-returns-failed-to-create-lock-directory

LanaZet commented 2 years ago

@mdhall272 Thank you! Problem was solved. Now im facing a new one: i trying to use .bam and .fasta files from /ExampleInputData; copied that folder, paste there phyloscanner_make_trees.py, exec command phyloscanner_make_trees.py InputFileList.csv --windows 1,300 and got this

mdhall272 commented 2 years ago

It looks like the problem was just that there are no trees in one window - nothing to worry about if the others were output properly?

BDI-pathogens / phyloscanner

Error on instaling progject dependencies #67