I'm posting this question to document the solution to a problem which had me stuck for several weeks for which no answer was found on StackExchange or discussion boards. (Answer forthcoming) I'm trying to run a compiled matlab program (MATLAB 2017a) compiled using the application compiler toolbox (Matlab compiler 6.4) on a Centos7 operating system. The tricky part is that my Matlab program uses the "system" command to call R and knit an rmarkdown document. To get standalone matlab programs to run on linux operating systems it is necessary to set LD_LIBRARY_PATH like thus:

export LD_LIBRARY_PATH={$LD_LIBRARY_PATH}:/usr/local/MATLAB/MATLAB_Runtimev92/v92/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtimev92/v92/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtimev92/v92/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtimev92/v92/sys/opengl/lib/glnxa64

The problem was, this broke R in the following way:

In grDevices::png(f) :
  unable to load shared object '/usr/lib64/R/library/grDevices/libs//cairo.so':
  /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates

Testing the R code independently I found it ran fine when run with sudo privileges. This didn't work because the MATLAB program wouldn't work when run with sudo privileges. Turns out, sudo privileges clear LD_LIBRARY_PATH: https://unix.stackexchange.com/questions/171262/ld-library-path-always-blank-after-sudo One workaround I found was to change my system call in MATLAB to call with sudo but its a sloppy fix since it requires the user to type their sudo password halfway through the program run. So I'm looking for a better fix.

How do I specify the **working directory** for **gnuplot** in interactive mode? If I want to call a script with "call 'label_loop.gnu'" and do not want to put the script file in the gnuplot installation folder, do I need to specify the full path each time? I think the following would be the case with normal usage. "I put the data or script I want to load in any directory"-> "I plot it in interactive mode"-> "I want to adjust the position of the label (preferably) with the mouse action"- > "I copy and paste the previous commands and I create a batch file"-> "GnuPlot converts the output to PDF"

I have this version of Ubuntu

Distributor ID:	Ubuntu
Description:	Ubuntu 18.04.3 LTS
Release:	18.04
Codename:	bionic

on my computer in a dual boot with Windows. I have tried to install R following this tutorial https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04 and I got the following error:

Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-base : Depends: r-base-core (>= 3.6.2-1bionic) but it is not going to be installed
          Depends: r-recommended (= 3.6.2-1bionic) but it is not going to be installed
          Recommends: r-base-html but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

To fix the error I followed this answer https://askubuntu.com/questions/140246/how-do-i-resolve-unmet-dependencies-after-adding-a-ppa but none of the proposed solution works. In partcular, even if my

apt-get -f install

returns

upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

, if I try again

apt install r-base

it's still not working

I am installing the R package (R-3.0.1) in Red Hat Linux 6.0. Initially when I tried to install it gave the error “F77 compiler not found”. I installed the compiler and tried it again, now the error I am getting is configure: error: --with-readline=yes (default) and headers/libs are not available I tried ./configure --with-x=no but it doesn't work, again I am getting the same error.

I want to find a gunzipped tarball file within my directory and unpack it. I have tried:

system("find . -name '*.gz' | tar -xvf -")

this produces the following error:

tar: Missing type keyword in mtree specification
x ./Library/rmarkdown_2.17.1.tar.gz
tar: Error exit delayed from previous errors.

system is a func in R to call linux commands.

I have a R-script which runs multiple files say file=1 to 50. I usually submit repeated jobs say 5 times with 10 files each time by changing the number in R-script. So, how can I submit the 5-job at once without submitting the job 5 times? In addition, I want to update the **default.out** and **errorfile** for each job. sample bash code:

#!/bin/bash

#PBS -l nodes=1:ppn=20,walltime=05:00:00

#PBS -m e
#PBS -o default.out
#PBS -e errorfile

module load R/4.0

Rscript ~/r_script1.R

My computer has Linux Mint 19.1 Tessa with R version 3.6.3. I am trying to do sudo apt-get update and I am having this error:

Err:21 https://cloud.r-project.org/bin/linux/ubuntu  bionic Release             
  404  Not Found [IP: 2600:9000:2045:e400:6:c2d3:f940:93a1 443]
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu  bionic Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.

Also, I would like to install appropriate drivers but I am also getting this error:

E:The repository 'https://cloud.r-project.org/bin/linux/ubuntu  bionic Release' does not have a Release file.

` Could someone help me? I remember that I had a problem upgrading R, but I am not sure what happened with Release. R now is working normally I think.

I am running interactive R in terminal, however it doesn't use all of the width of the terminal. It only use 72 characters out of 226. It is very uncomfortable to read any data with a lot of columns displayed in interactive R. I am using urxvt on debian 9,8.

I want to loop over a dataframe, I want to compare one of the elements of the actual row and the next row. for example, I have a data frame that looks like this: V1 V2 V3 V4 1 chr1 10 1000 2000 2 chr1 10 2000 3000 3 chr1 10 4000 5000 . . . I would like to compare the element of the 1st row and 4th column with the element of the 2nd row and third column, and if they are the same do something, then the element of the 2nd row and 4th column with the element of the 3th row and 3th column, do something and so on. So I am trying something like this: for (i in 1:nrow(my_dataframe)){ if (my_dataframe[i, 4] == my_dataframe[i+1 , 3]) { print("OK") } } So this would give me for example 1 OK with my example data frame However it looks that R doesn't like the i + 1, because is giving me the next error: Error in if (tabla4subset[i, 4] > tabla4subset[i + 1, 3]) { : missing value where TRUE/FALSE needed Some one know how to do this?

After 10+ years using debian-based linux, I am now using Arch. I use R for data science analysis and development. I am facing difficulties to install the R package ragg (r-ragg), which is a dependency for other libraries I use. When I try to install "ragg" from within R using the install.packages("ragg") command, I get the following error: make: * [/usr/lib64/R/etc/Makeconf:204: agg/src/agg_font_freetype.o] Error 1 which leads to a compilation failure for "ragg". I got the same error message in Arch and in an arch-based OS Any suggestion to resolve this? (I have search a lot how to solve this, without concrete success.) I also tried to install it via terminal using yay -S r-ragg and I received this as feedback:

make: *** [/usr/lib64/R/etc/Makeconf:204: agg/src/agg_font_freetype.o] Error 1
ERROR: compilation failed for package ‘ragg’
removing ‘/home/machiavelli/.cache/yay/r-ragg/src/build/ragg’
==> ERROR: A failure occurred in build().
Aborting...
-> error making: r-ragg-exit status 4
-> Failed to install the following packages. Manual intervention is required:
r-ragg - exit status 4

The relevant part of the Makeconf file is:

$ awk 'NR>200 && NR $@
.cpp.d:
	@echo "making $@ from $ install.packages("ragg")

* installing *source* package ‘ragg’ ...
** package ‘ragg’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/sysprof-6 -pthread
Using PKG_LIBS=-lfreetype -lpng16 -ltiff -ljpeg
** libs
using C++ compiler: ‘g++ (GCC) 14.2.1 20240805’

[endless compilation verbose here]

agg/src/agg_font_freetype.cpp: In instantiation of ‘bool agg::decompose_ft_outline(const FT_Outline&, bool, const trans_affine&, PathStorage&) [with PathStorage = path_storage_integer; FT_Outline = FT_Outline_]’:
agg/src/agg_font_freetype.cpp:1071:48:   required from here
 1071 |                         if(decompose_ft_outline(m_cur_face->glyph->outline,
      |                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1072 |                                                 m_flip_y,
      |                                                 ~~~~~~~~~
 1073 |                                                 m_affine,
      |                                                 ~~~~~~~~~
 1074 |                                                 m_path32))
      |                                                 ~~~~~~~~~
agg/src/agg_font_freetype.cpp:182:35: error: invalid conversion from ‘unsigned char*’ to ‘char*’ [-fpermissive]
  182 |             tags  = outline.tags  + first;
      |                     ~~~~~~~~~~~~~~^~~~~~~
      |                                   |
      |                                   unsigned char*
agg/src/agg_font_freetype.cpp: In instantiation of ‘bool agg::decompose_ft_outline(const FT_Outline&, bool, const trans_affine&, PathStorage&) [with PathStorage = path_storage_integer; FT_Outline = FT_Outline_]’:
agg/src/agg_font_freetype.cpp:1092:48:   required from here
 1092 |                         if(decompose_ft_outline(m_cur_face->glyph->outline,
      |                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1093 |                                                 m_flip_y,
      |                                                 ~~~~~~~~~
 1094 |                                                 m_affine,
      |                                                 ~~~~~~~~~
 1095 |                                                 m_path16))
      |                                                 ~~~~~~~~~
agg/src/agg_font_freetype.cpp:182:35: error: invalid conversion from ‘unsigned char*’ to ‘char*’ [-fpermissive]
  182 |             tags  = outline.tags  + first;
      |                     ~~~~~~~~~~~~~~^~~~~~~
      |                                   |
      |                                   unsigned char*
make: *** [/usr/lib64/R/etc/Makeconf:204: agg/src/agg_font_freetype.o] Error 1
ERROR: compilation failed for package ‘ragg’

----- **ISSUE RESOLVED** install.packages("ragg") downloads and installs (or fails to install, in my case) ragg version 1.3.2 from CRAN. This was not working on my workstation running arch-based Endeavour OS. I found the source code for ragg version 1.3.2.9000 at https://r-lib.r-universe.dev/ragg\ and it worked like a charm. No compilation needed, instant success. I loaded the library and ran a test code and it produced the expected output. Case closed. Many thanks for your support through this!

Fetch data based on date(column 1) and time (column 2). Each date has time in column 2. Based on each date in column1 two files are to be generated which will have all the fields based on time 6:00 to 21:50:08 (day) and 22:00:00 to 5:50:00 (night). Trying to get two files for each date as date_day and date_night based on the times specified. Input file:

Date       Time     R1      R2      R3
03/10/2023 19:00:08	19.06	39.870	5.12
03/10/2023 19:10:08	18.87	39.970	4.98
03/10/2023 19:20:08	18.68	39.940	4.80
03/10/2023 19:30:08	18.84	40.110	5.01
03/10/2023 19:40:08	18.89	38.960	4.64
03/10/2023 19:50:08	18.60	39.100	4.43
03/10/2023 23:30:08	18.03	34.200	2.03
03/10/2023 23:40:08	17.94	33.930	1.84
03/10/2023 23:50:08	17.87	33.840	1.74
03/11/2023 00:00:08	17.75	33.790	1.61
03/11/2023 00:10:08	17.96	34.060	1.91
03/11/2023 00:20:08	18.13	33.690	1.91
03/11/2023 00:30:08	17.91	33.620	1.68

Output files: 03/10/2023_day

Date        Time    R1      R2      R3
03/10/2023 19:00:08	19.06	39.870	5.12
03/10/2023 19:10:08	18.87	39.970	4.98
03/10/2023 19:20:08	18.68	39.940	4.80
03/10/2023 19:30:08	18.84	40.110	5.01
03/10/2023 19:40:08	18.89	38.960	4.64

03/10/2023_night

Date        Time     R1      R2      R3
03/10/2023 19:50:08	18.60	39.100	4.43
03/10/2023 23:30:08	18.03	34.200	2.03
03/10/2023 23:40:08	17.94	33.930	1.84
03/10/2023 23:50:08	17.87	33.840	1.74

03/11/2023_night:

Date       Time      R1     R2      R3
03/11/2023 00:00:08	17.75	33.790	1.61
03/11/2023 00:10:08	17.96	34.060	1.91
03/11/2023 00:20:08	18.13	33.690	1.91
03/11/2023 00:30:08	17.91	33.620	1.68

I tried the following to fetch day and night files. This I will have to do for each date again and again. I removed the ':' from the time column in my code to get a number without :. Can anyone please help to put it in a loop and the separate day and night files for each date? awk '$1 ~ /03\/10\/2023/ && $2 >= 060000 && $2 03_10_23_day.csv awk '$1 ~ /03\/10\/2023/ && $2 > 215000' data |sed 's/\t/,/g' > 03_10_23_night.csv

I'm facing an issue with SSH on a server. Running individual scripts (source s01.sh, etc.) works fine, with errors displayed in the console. However, when using a master script to source these scripts, the SSH connection unexpectedly terminates upon encountering an error. The master script master.sh is as follows: #!/bin/bash set -e source s01.sh source s02.sh Rscript s03.R source s04.sh I source the master script in interactive SSH session using source master.sh With set -e, I expect the script to stop at errors, but instead, it's causing the entire SSH session to drop. This only happens with the combined script, not with individual sourcing. Why does this occur, and how can I keep the SSH session from closing on script errors? I am aware this might involve SSH server configurations, but I'm unsure which settings to investigate.

1. Debian 11 only updates to R 4.0.4. 2. I have packages that require at least R 4.1.0 to be installed. 4. I already tried adding the official R repository to the source list as the official website tells to do , but I get the following limitation. > sudo apt update > > 20 packages can be upgraded. Run 'apt list --upgradable' to see them. > > apt list --upgradable > > r-base-core/bullseye-cran40 4.3.2-1~bullseyecran.0 amd64 [upgradable from: 4.0.4-1] > > r-base-dev/bullseye-cran40 4.3.2-1~bullseyecran.0 all [upgradable from: 4.0.4-1] > > r-base/bullseye-cran40 4.3.2-1~bullseyecran.0 all [upgradable from: 4.0.4-1] > > r-cran-boot/bullseye-cran40 1.3-28.1-1~bullseyecran.0 all [upgradable from: 1.3-27-1] > > r-cran-class/bullseye-cran40 7.3-22-2~bullseyecran.0 amd64 [upgradable from: 7.3-18-1] > > r-cran-cluster/bullseye-cran40 2.1.4-1~bullseyecran.0 amd64 [upgradable from: 2.1.1-1] > > r-cran-codetools/bullseye-cran40 0.2-19-1~bullseyecran.0 all [upgradable from: 0.2-18-1] > > r-cran-foreign/bullseye-cran40 0.8.85-1~bullseyecran.0 amd64 [upgradable from: 0.8.81-1] > > r-cran-kernsmooth/bullseye-cran40 2.23-22-1~bullseyecran.0 amd64 [upgradable from: 2.23-18-1] > > r-cran-lattice/bullseye-cran40 0.22-5-1~bullseyecran.0 amd64 [upgradable from: 0.20-41-1+b1] > > r-cran-littler/bullseye-cran40 0.3.18-2~bullseyecran.0 amd64 [upgradable from: 0.3.12-1] > > r-cran-mass/bullseye-cran40 7.3-60-2~bullseyecran.0 amd64 [upgradable from: 7.3-53.1-1] > > r-cran-matrix/bullseye-cran40 1.6-1.1-1~bullseyecran.0 amd64 [upgradable from: 1.3-2-1] > > r-cran-mgcv/bullseye-cran40 1.9-0-1~bullseyecran.0 amd64 [upgradable from: 1.8-34-1] > > r-cran-nlme/bullseye-cran40 3.1.163-1~bullseyecran.0 amd64 [upgradable from: 3.1.152-1] > > r-cran-nnet/bullseye-cran40 7.3-19-2~bullseyecran.0 amd64 [upgradable from: 7.3-15-1] > > r-cran-rpart/bullseye-cran40 4.1.21-1~bullseyecran.0 amd64 [upgradable from: 4.1-15-2+b1] > > r-cran-spatial/bullseye-cran40 7.3-17-1~bullseyecran.0 amd64 [upgradable from: 7.3-13-1] > > r-cran-survival/bullseye-cran40 3.5-7-1~bullseyecran.0 amd64 [upgradable from: 3.2-7-1] > > r-recommended/bullseye-cran40 4.3.2-1~bullseyecran.0 all [upgradable from: 4.0.4-1] > > sudo apt upgrade > > The following packages have been kept back: > > r-base r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-littler > > r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended >

I am trying to install R in our cluster (the cluster is Red Hat Enterprise Linux 6), where I don't have root access. I tried: $wget http://cran.rstudio.com/src/base/R-3/R-3.1.1.tar.gz $ tar xvf R-3.1.1.tar.gz $ cd R-3.1.1 $ ./configure --prefix=/home/Kryo/R-3.1.1 But I am getting an error: configure: error: --with-x=yes (default) and X11 headers/libs are not available

# Problem I would like to use ansible to provision a virtual box. This box will need to do multiple things, but it needs to have R installed as well as some specific packages that aren't included in base R. I use the vagrant file provided below to create a new virtual machine and then install ansible, epel-release and git using yum. On this virtual machine I then use the "Alma Linux 8" and "Docker" playbooks provided below before the one I believe to be problematic. I then run this playbook to install R --- - name: "Setup R on the local machine" hosts: localhost connection: local tasks: # Update all installed packages - name: Update all packages to their latest version become: yes ansible.builtin.package: name: "*" state: latest # Install EPEL to get extra packages - name: Install EPEL become: yes ansible.builtin.package: name: epel-release state: latest # Enable the Code Ready Builder (CRB) repository - name: Install utilities to enable package repositories become: yes ansible.builtin.package: name: yum-utils state: latest - name: Enable the PowerTools repository become: yes shell: dnf config-manager --set-enabled powertools # Install R - name: Install R become: yes ansible.builtin.package: name: R state: latest After running this playbook I can then run the command Rscript --slave --no-save --no-restore-history -e "print('Test')" "Test" showing that R is working at least in some capacity. But then when I try and use this to install a package I get this error Rscript --slave --no-save --no-restore-history -e "install.packages('tidyverse')" > Installing package into ‘/usr/lib64/R/library’ > (as ‘lib’ is unspecified) > Warning in install.packages("tidyverse") : > 'lib = "/usr/lib64/R/library"' is not writable > Error in install.packages("tidyverse") : unable to install packages > Execution halted # Attempted Fix # I have attempted to fix this by appending these lines on to the end of the R playbook above - name: Make directory writable become: yes file: path: /usr/lib64/R/library mode: '0777' - name: Make directory writable become: yes file: path: /usr/share/doc/R/html mode: '0777' to manually make the problematic directories readable, but this has not worked. # Reference Files # ## Vagrant File ## Vagrant.configure("2") do |config| config.vm.box = "almalinux/8" config.vm.provider "virtualbox" do |vb| vb.memory = "2048" vb.cpus = 2 end end ## Ansible Playbooks ## ### Alma Linux 8 ### --- - name: "Setup AlmaLinux 8 on the local machine" hosts: localhost connection: local tasks: # Install the base operating systemctl - name: Update all packages to their latest versions become: yes ansible.builtin.package: name: '*' state: latest - name: Install virtual machine support become: yes ansible.builtin.package: name: open-vm-tools state: latest # Install EPEL to get extra packages - name: Install EPEL become: yes ansible.builtin.package: name: epel-release state: latest ### Docker ### --- - name: "Setup Docker on the local machine" hosts: localhost connection: local tasks: # Install Docker - name: Uninstall any older versions of Docker become: yes ansible.builtin.package: name: - docker - docker-client - docker-client-latest - docker-common - docker-latest - docker-latest-logrotate - docker-logrotate - docker-engine state: absent - name: Install yum-utils to install a new package repository become: yes ansible.builtin.package: name: yum-utils state: latest - name: Install the Docker Repository become: yes shell: yum-config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo - name: Install Docker become: yes ansible.builtin.package: name: - docker-ce - docker-ce-cli - containerd.io - docker-buildx-plugin - docker-compose-plugin state: latest - name: Enable the docker service become: yes shell: systemctl enable docker - name: Enable the containerd service become: yes shell: systemctl enable containerd - name: Start the docker service become: yes shell: systemctl start docker - name: Start the containerd service become: yes shell: systemctl start containerd - name: Ensure docker group exists become: yes ansible.builtin.group: name: docker state: present - name: Add the vagrant user to the docker group become: yes ansible.builtin.user: name: vagrant groups: docker append: yes

I'm sorry for having written such a long question, but given how many times similar questions have been asked, I felt like I had to give a lot more context. ---- In my system, I get. . .

checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 8.2.1
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.28.0... 
configure: error: libcurl >= 7.28.0 library and headers are required with support for https

when trying to install R (**version 4.0.3**, this is non-negotiable) with ./configure --prefix=/opt/R/ --exec-prefix=/opt/R/ --with-libpth-prefix=/opt/ --without-recommended-packages --with-pcre1 --enable-R-shlib. In config.log, I see the following.

configure:46024: checking for curl-config
configure:46042: found /usr/bin/curl-config
configure:46054: result: /usr/bin/curl-config
configure:46080: checking curl/curl.h usability
configure:46080: gcc -c  -g -O2 -fpic  -I/usr/local/include  conftest.c >&5
configure:46080: $? = 0
configure:46080: result: yes
configure:46080: checking curl/curl.h presence
configure:46080: gcc -E  -I/usr/local/include  conftest.c
configure:46080: $? = 0
configure:46080: result: yes
configure:46080: checking for curl/curl.h
configure:46080: result: yes
configure:46094: checking if libcurl is version 7 and >= 7.28.0
configure:46123: gcc -o conftest  -g -O2 -fpic  -I/usr/local/include  -L/usr/local/lib64 conftest.c -lcurl -lpcre -llzma -lbz2 -lz -lrt -ldl -lm  >&5
configure:46123: $? = 0
configure:46123: ./conftest
configure:46123: $? = 1
configure: program exited with status 1
configure: failed program was:

And then, after the contents of confdefs.h have been exposed, I see:

#include 
| #include 
| int main()
| {
| #ifdef LIBCURL_VERSION_MAJOR
| #if LIBCURL_VERSION_MAJOR > 7
|   exit(1);
| #elif LIBCURL_VERSION_MAJOR == 7 && LIBCURL_VERSION_MINOR >= 28
|   exit(0);
| #else
|   exit(1);
| #endif
| #else
|   exit(1);
| #endif
| }
| 
configure:46133: result: 
configure:46191: error: libcurl >= 7.28.0 library and headers are required with support for https

There are multiple questions concerning the same error across multiple websites, but none of the solutions I tried worked for me. Since apparently I have multiple versions of available. . .

bash-4.2# yum list curl --showduplicates | head -n 5

Loaded plugins: ovl, priorities
Installed Packages
curl.x86_64                    8.2.1-1.amzn2.0.3                      installed 
Available Packages
curl.x86_64                    7.55.1-8.amzn2.0.1                     amzn2-core

bash-4.2# yum list libcurl --showduplicates | head -n 5

Loaded plugins: ovl, priorities
Installed Packages
libcurl.x86_64                  8.2.1-1.amzn2.0.3                     installed 
Available Packages
libcurl.x86_64                  7.55.1-8.amzn2.0.1                    amzn2-core

. . . (I have many more of each), my last tries have revolved around trying to downgrade and/or remove curl and libcurl, but no luck:

bash-4.2# yum downgrade libcurl
Loaded plugins: ovl, priorities
amzn2-core                                                                                                                                                                                  | 3.6 kB  00:00:00     
Resolving Dependencies
--> Running transaction check
---> Package libcurl.x86_64 0:8.2.1-1.amzn2.0.2 will be a downgrade
---> Package libcurl.x86_64 0:8.2.1-1.amzn2.0.3 will be erased
--> Finished Dependency Resolution
Error: Package: curl-8.2.1-1.amzn2.0.3.x86_64 (installed)
           Requires: libcurl(x86-64) = 8.2.1-1.amzn2.0.3

(The output continues). I'm working in a docker container, so the above is easily reproducible. I leave the Docker file at the end of this question. I presume the following is useful system information.

bash-4.2# cat /etc/*-release*

NAME="Amazon Linux"
VERSION="2"
ID="amzn"
ID_LIKE="centos rhel fedora"
VERSION_ID="2"
PRETTY_NAME="Amazon Linux 2"
ANSI_COLOR="0;33"
CPE_NAME="cpe:2.3:o:amazon:amazon_linux:2"
HOME_URL="https://amazonlinux.com/ "
SUPPORT_END="2025-06-30"
Amazon Linux release 2 (Karoo)
cpe:2.3:o:amazon:amazon_linux:2

Can anyone help me fix this? ---- Here's Dockerfile:

FROM amazonlinux:2

RUN yum update -y && \
    yum install -y make zip gzip tar which wget java \
    readline-devel \
    xorg-x11-server-devel libX11-devel libXt-devel \
    libcurl-devel libcurl4-openssl-dev \
    openssl-devel libxml2-devel \
    gcc-c++ gcc-gfortran \
    zlib-devel bzip2 bzip2-libs bzip2-devel xz-devel && \
    yum clean all

RUN mkdir -p /opt/R /opt/bin

RUN mv /usr/bin/which /opt/bin/

WORKDIR /opt
RUN wget https://cran.r-project.org/src/base/R-4/R-4.0.3.tar.gz  && \
    tar -xf R-4.0.3.tar.gz && \
    mv R-4.0.3/* /opt/R && \
    rm -rf R-4.0.3.tar.gz R-4.0.3

WORKDIR /opt/R

# RUN ./configure --prefix=/opt/R/ --exec-prefix=/opt/R/ --with-libpth-prefix=/opt/ \
#     --without-recommended-packages --with-pcre1 --enable-R-shlib

CMD ["bash"]

I've been having troubles with installing the tidyverse package in Rstudio and more recently when reinstalling R. I'll post my most recent error message when reinstalling R below after system info. My system info to start: Lenovo Thinkpad T14s Gen 2a OS:Dual boot with Linux Mint Cinnamon 20.3 (una)(kernel 5.13.0-51-generic), and Windows 10 on separate partition. userXXXX:~$ sudo apt install --no-install-recommends r-cran-tidyverse Reading package lists... Done Building dependency tree Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help resolve the situation: The following packages have unmet dependencies: r-cran-tidyverse : Depends: r-cran-broom but it is not going to be installed Depends: r-cran-dbplyr but it is not going to be installed Depends: r-cran-dplyr but it is not going to be installed Depends: r-cran-dtplyr but it is not going to be installed Depends: r-cran-forcats but it is not going to be installed Depends: r-cran-googledrive but it is not going to be installed Depends: r-cran-googlesheets4 but it is not going to be installed Depends: r-cran-ggplot2 but it is not going to be installed Depends: r-cran-haven but it is not going to be installed Depends: r-cran-hms but it is not going to be installed Depends: r-cran-httr but it is not going to be installed Depends: r-cran-modelr but it is not going to be installed Depends: r-cran-readr but it is not going to be installed Depends: r-cran-readxl but it is not going to be installed Depends: r-cran-reprex but it is not going to be installed Depends: r-cran-rvest but it is not going to be installed Depends: r-cran-stringr but it is not going to be installed Depends: r-cran-tibble but it is not going to be installed Depends: r-cran-tidyr but it is not going to be installed E: Unable to correct problems, you have held broken packages. It seems like I need to remove these broken packages before reinstalling the new ones. If there is anyone that can help with going about this it would be greatly appreciated! Thank you!

I am trying to do a build and local install of R 4.0.4 on Red Hat Linux 6.8. There were several unmet dependencies which I resolved by doing local installations (following the procedure in this ). However, I couldn't resolve the issue of pcre2 with that procedure. This is the configure command I run: ./configure --with-pcre2 --prefix=$HOME/bin/R-4.0.4 --enable-R-shlib LDFLAGS="-L/$HOME/local/zlib-1.2.11/lib -L/$HOME/local/bzip2-1.0.8/lib -L/$HOME/local/xz-5.2.5/lib -L/$HOME/local/pcre2-10.00/lib" CPPFLAGS="-I/$HOME/local/zlib-1.2.11/include" This is the error I get: checking whether PCRE support suffices... no configure: error: PCRE2 library and headers are required, or use --with-pcre1 and PCRE >= 8.32 with UTF-8 support I also tried configure with a local installation of pcre-8.44 and --with-pcre1 flag but I get the same error. What should I do so that the configure script detects the pcre2 local installation?

I have a multi-user installation of nix on ubuntu 22.04. I'm trying to develop an R package that depends on data.table, but am unable to install data.table with zlib headers so that I can use the fwrite function with gzip compression. Here is the default.nix I'm using with direnv:

with import  {};

let
    rlibs = with rPackages; [
      R
      Rcpp
      data_table
      roxygen2
      pkgbuild
    ];

    _libs = with pkgs; [
        zlib
        ccls
    ];

in mkShell {
    nativeBuildInputs = [
      rlibs
      _libs
    ];
}

Everything installs fine and runs, but when I call fwrite(iris, "iris.txt.gz', compress="gzip") I get Compression in fwrite uses zlib library. Its header files were not found at the time data.table was compiled. To enable fwrite compression, please reinstall data.table and study the output for further guidance. At first I didn't have zlib in default.nix so I added it and tried reinstalling. This required cleaning out the full set of packages. I can do nix-store --delete, but it also makes me garbage collect all the specified packages. Reinstaling did not solve the problem though. I don't see any output to inspect either. How do I specify zlib as a dependency? Also is there a way to re-install a package with nix? I can't find any documentation online about it - any results are about reinstalling nix as a whole, not a single package. UPDATE: I've also tried nix-shell -p pkg-config zlib R rPackages.data_table. During the data.table install, there are messages that pkg-config was not found. However, in that shell, running pkg-config --libs zlib gives -L/nix/store/37a5krk4a1a8vhl93q2bm9nbv8hymyii-zlib-1.2.13/lib -lz Trying the nix manuals override doesn't work either:

{
    packageOverrides = super: let self = super.pkgs; in
    {

        rEnv = super.rWrapper.override {
            packages = with self.rPackages; [
                data_table
                ];
        };
    };
}

I have a bash script that loops over iterations. How do i save the output from the individual scripts in the bash file according to the iteration? #Working directory cd /lustre/nobackup/WUR/ABGC/agyir001/ # Set the number of replicates num_replicates=100 # Loop over the replicates for i in $(seq 1 $num_replicates); do # replicate number with leading zeros rep_num=$(printf "%03d" $i) output_file="accuracy_results_${rep_num}.txt" #Run scenario 1,2 and 3 of male contributions Rscript Scenario_1_male_contributions.R Rscript Scenario_2_male_contributions.R Rscript Scenario_3_male_contributions.R #creating correlated qtl effects for 1000 selected qtls Rscript Correlated_qtl_effects.R #Selecting 1000 qtls, creating TBVS and phenotypes Rscript Breeding_values_and_Phenotypes.R 7500 # prepare phenotypes and genotypes/markers Rscript /lustre/nobackup/WUR/ABGC/agyir001/scripts/Markers_phenotypes_for_EBV.R