下载R包的时候出现了报错

Question

下载R包的时候出现了报错

先是下载scater包失败

-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find one of freetype2 libpng libtiff-4 libjpeg. Try installing:
 * deb: libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev (Debian, Ubuntu, etc)
 * rpm: freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel (Fedora, CentOS, RHEL)
 * csw: libfreetype_dev libpng16_dev libtiff_dev libjpeg_dev (Solaris)
If freetype2 libpng libtiff-4 libjpeg is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a freetype2 libpng libtiff-4 libjpeg.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
In file included from /mnt/share/rxj/miniconda3/envs/rna/x86_64-conda-linux-gnu/sysroot/usr/include/features.h:361,
                 from /mnt/share/rxj/miniconda3/envs/rna/x86_64-conda-linux-gnu/sysroot/usr/include/limits.h:27,
                 from /mnt/share/rxj/miniconda3/envs/rna/lib/gcc/x86_64-conda-linux-gnu/13.1.0/include/limits.h:205,
                 from /mnt/share/rxj/miniconda3/envs/rna/lib/gcc/x86_64-conda-linux-gnu/13.1.0/include/syslimits.h:7,
                 from /mnt/share/rxj/miniconda3/envs/rna/lib/gcc/x86_64-conda-linux-gnu/13.1.0/include/limits.h:34,
                 from /usr/include/libpng16/pngconf.h:30,
                 from /usr/include/libpng16/png.h:366,
                 from <stdin>:2:
/usr/include/x86_64-linux-gnu/sys/cdefs.h:467:49: error: missing binary operator before token "("
  467 | #if __GNUC_PREREQ (4,8) || __glibc_clang_prereq (3,5)
      |                                                 ^
In file included from /mnt/share/rxj/miniconda3/envs/rna/x86_64-conda-linux-gnu/sysroot/usr/include/stdio.h:932,
                 from /usr/include/libpng16/pngconf.h:45:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:225:17: error: missing binary operator before token "("
  225 | #if __GLIBC_USE (DEPRECATED_GETS)
      |                 ^
--------------------------------------------------------------------
ERROR: configuration failed for package ‘ragg’
* removing ‘/mnt/share/rxj/miniconda3/envs/rna/lib/R/library/ragg’
ERROR: dependency ‘ragg’ is not available for package ‘ggrastr’
* removing ‘/mnt/share/rxj/miniconda3/envs/rna/lib/R/library/ggrastr’
ERROR: dependency ‘ggrastr’ is not available for package ‘scater’
* removing ‘/mnt/share/rxj/miniconda3/envs/rna/lib/R/library/scater’

The downloaded source packages are in
        ‘/tmp/RtmpVZLpGT/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(...) :
  installation of package ‘ragg’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘ggrastr’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘scater’ had non-zero exit status

以为是ragg，ggrastr,scater版本不适配，想删掉重新下载，结果相应的路径里就没有，我就直接下载了ragg。

结果在下载ragg时出现又报错。

 install.packages("/mnt/share/rxj/ragg_1.2.5.tar.gz",repos=NULL)
* 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/x86_64-linux-gnu
Using PKG_LIBS=-lfreetype -lpng16 -lz -ltiff -ljpeg -ljpeg
-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find one of freetype2 libpng libtiff-4 libjpeg. Try installing:
 * deb: libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev (Debian, Ubuntu, etc)
 * rpm: freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel (Fedora, CentOS, RHEL)
 * csw: libfreetype_dev libpng16_dev libtiff_dev libjpeg_dev (Solaris)
If freetype2 libpng libtiff-4 libjpeg is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a freetype2 libpng libtiff-4 libjpeg.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
In file included from /mnt/share/rxj/miniconda3/envs/rna/x86_64-conda-linux-gnu/sysroot/usr/include/features.h:361,
                 from /mnt/share/rxj/miniconda3/envs/rna/x86_64-conda-linux-gnu/sysroot/usr/include/limits.h:27,
                 from /mnt/share/rxj/miniconda3/envs/rna/lib/gcc/x86_64-conda-linux-gnu/13.1.0/include/limits.h:205,
                 from /mnt/share/rxj/miniconda3/envs/rna/lib/gcc/x86_64-conda-linux-gnu/13.1.0/include/syslimits.h:7,
                 from /mnt/share/rxj/miniconda3/envs/rna/lib/gcc/x86_64-conda-linux-gnu/13.1.0/include/limits.h:34,
                 from /usr/include/libpng16/pngconf.h:30,
                 from /usr/include/libpng16/png.h:366,
                 from <stdin>:2:
/usr/include/x86_64-linux-gnu/sys/cdefs.h:467:49: error: missing binary operator before token "("
  467 | #if __GNUC_PREREQ (4,8) || __glibc_clang_prereq (3,5)
      |                                                 ^
In file included from /mnt/share/rxj/miniconda3/envs/rna/x86_64-conda-linux-gnu/sysroot/usr/include/stdio.h:932,
                 from /usr/include/libpng16/pngconf.h:45:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:225:17: error: missing binary operator before token "("
  225 | #if __GLIBC_USE (DEPRECATED_GETS)
      |                 ^
--------------------------------------------------------------------
ERROR: configuration failed for package ‘ragg’
* removing ‘/mnt/share/rxj/miniconda3/envs/rna/lib/R/library/ragg’
Warning message:
In install.packages("/mnt/share/rxj/ragg_1.2.5.tar.gz", repos = NULL) :
  installation of package ‘/mnt/share/rxj/ragg_1.2.5.tar.gz’ had non-zero exit status

最后的ERROR，我尝试移除ragg，结果在显示的路径里也没有ragg。
我完全不知道如何解决，麻烦各位帮忙看看

Answer 1

采用chatgpt：
根据报错信息来看，你在下载 R 包时遇到了一些依赖问题，特别是与 freetype2, libpng, libtiff-4, 和 libjpeg 相关的依赖。这些依赖在你的系统中似乎未正确配置或安装，导致下载 scater 和 ragg 包失败。

以下是解决方案的步骤：

安装依赖项：
根据报错信息，你需要安装一些系统依赖项，这可以在终端中通过以下命令完成。以 Debian/Ubuntu 系统为例，执行：

sudo apt-get update
sudo apt-get install -y libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev

如果你使用的是 Fedora/CentOS/RHEL 等系统，可以尝试执行以下命令：

sudo yum install -y freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel

设置 pkg-config：
如果你仍然遇到问题，可能是由于 pkg-config 没有正确配置。确保 pkg-config 在你的 PATH 中，并且 PKG_CONFIG_PATH 包含了正确的路径。你可以使用以下命令检查：

echo $PKG_CONFIG_PATH

如果它为空，你可以手动设置 PKG_CONFIG_PATH，例如：

export PKG_CONFIG_PATH="/usr/lib/pkgconfig:/usr/local/lib/pkgconfig"

重新安装 R 包：
完成上述步骤后，再次尝试下载和安装 scater 和 ragg 包：

install.packages("scater")
install.packages("/mnt/share/rxj/ragg_1.2.5.tar.gz", repos = NULL, type = "source")

安装 ragg 时需要指定 type = "source" 参数，因为你使用了本地的 tar.gz 文件。

如果一切顺利，你应该能够成功安装这些 R 包。