如何在@INC错误中恢复Can't locate IO/Zlib.pm？

Question

我安装了这个库：https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network/affymetrix-devnet-tools.html

使用：

install.packages("SNPolisher_2.0.3.tar.gz",repos=NULL,type="source")

我正在使用R版本3.6.3运行它，如下所示：

> library(SNPolisher)
> Ps_Visualization(pidFile="pidfile.txt", summaryFile="brlmm-p.summary.txt" ,callFile="brlmm-p.calls.txt", confidenceFile="brlmm-p.confidences.txt")
Can't locate IO/Zlib.pm in @INC (@INC contains: /software/linux-el7-x86_64/tools/vcftools-0.1.16/installer/vcftools-vcftools-954e607/src/perl /opt/moab/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/anamaria/R/x86_64-pc-linux-gnu-library/3.6/SNPolisher/Perl/visualization.pl line 9.
BEGIN failed--compilation aborted at /home/anamaria/R/x86_64-pc-linux-gnu-library/3.6/SNPolisher/Perl/visualization.pl line 9.
1 probesets in the pid file.  First 1 requested for plotting. Generating the cluster plots for 1 SNPs/probesets.


No file found for ABAFT_g_4RWG569_BI_SNP_A01_34952.CEL in the temporary directory Temp 

Note that ABAFT_g_4RWG569_BI_SNP_A01_34952.CEL file is located in Temp and I also have it in the current directory from where I’m running this.

pidfile.txt看起来像这样：

probeset_id
ABAFT_g_4RWG569_BI_SNP_A01_34952.CEL

有关are软件的详细信息，请访问：https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017790_SNPolisher_UG.pdf

每个$KjetilS的更新。评论

perl -v
This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi
(with 33 registered patches, see perl -V for more detail)

perl -MIO::Zlib -le'print$INC{"IO/Zlib.pm"}'

 Can't locate IO/Zlib.pm in @INC (@INC contains: /software/linux-el7-x86_64/tools/vcftools-0.1.16/installer/vcftools-vcftools-954e607/src/perl /opt/moab/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .).

BEGIN失败--编译中止。

我不能使用“sudo”(或任何其他sudo命令)运行此命令，因为我在此群集上没有sys admin权限：

sudo perl -MIO::Zlib -le'print$INC{"IO/Zlib.pm"}'

I can not find library with:

find /software/linux-el7-x86_64/tools/vcftools-0.1.16/installer/vcftools-vcftools-954e607/src/perl /opt/moab/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 -wholename "*IO/Zlib.pm" -ls

find: ‘/opt/moab/lib/perl5’: No such file or directory
find: ‘/usr/local/lib64/perl5’: No such file or directory
find: ‘/usr/local/share/perl5’: No such file or directory

CentOS Linux release 7.4.1708 (Core) 
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)" 

Answer 1

我不知道R，但这看起来像是一条Perl错误消息。Perl找不到IO::Zlib模块。这是不寻常的，因为IO::Zlib是一个核心模块，因此是从Perl version5.9.3开始的任何常规perl安装的一部分。我会尝试的事情：

• 运行perl -v查看您是否获得了早于5.9.3的perl ( 2020年非常少见，因为该版本是在2006年发布的)
• 运行find /software/linux-el7-x86_64/tools/vcftools-0.1.16/installer/vcftools-vcftools-954e607/src/perl /opt/moab/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 -wholename "*IO/Zlib.pm" -ls并检查该Zlib.pm文件是否对当前用户可读。列出的目录是错误消息中列出的目录，如果该文件存在，但您的当前用户对该文件没有读取权限，请在front
• perl -MIO::Zlib -le'print$INC{"IO/Zlib.pm"}'
• sudo perl -MIO::Zlib -le'print$INC{"IO/Zlib.pm"}'中使用directories)
• sudo cpan IO::Zlib or
• sudo cpan App::cpanminus和sudo cpanm IO::Zlib
• export PERLLIB=/some/dir:$PERLLIB运行与上述相同的命令(sudo space)，如果您找到IO/Zlib. to文件，请将该权限添加到上面的chmod和zlib.to文件中。但它不在perl -V输出底部的@INC下面提到的目录下。PERLLIB中的目录不应该是IO目录，而是它正上方的目录。
• 您使用的是哪个linux版本和发行版，可能是

如果你添加了关于你正在运行的Linux版本和发行版的信息，你更有可能得到好的答案。在某些系统上，这是由cat /etc/*release揭示的