From mboxrd@z Thu Jan 1 00:00:00 1970 X-Msuck: nntp://news.gmane.io/gmane.text.pandoc/31979 Path: news.gmane.io!.POSTED.blaine.gmane.org!not-for-mail From: =?UTF-8?Q?J=C3=BAlia_Mir?= Newsgroups: gmane.text.pandoc Subject: how to solve libgmp.so.10 error inside a biocontainer Date: Thu, 12 Jan 2023 02:12:03 -0800 (PST) Message-ID: Reply-To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_Part_4340_1457680069.1673518323762" Injection-Info: ciao.gmane.io; posting-host="blaine.gmane.org:116.202.254.214"; logging-data="13925"; mail-complaints-to="usenet@ciao.gmane.io" To: pandoc-discuss Original-X-From: pandoc-discuss+bncBCM2VMOI6MCRB5NZ76OQMGQEYBFAMOQ-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org Thu Jan 12 11:12:09 2023 Return-path: Envelope-to: gtp-pandoc-discuss@m.gmane-mx.org Original-Received: from mail-oa1-f63.google.com ([209.85.160.63]) by ciao.gmane.io with esmtps (TLS1.3:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.92) (envelope-from ) id 1pFuZ6-0003MZ-MR for gtp-pandoc-discuss@m.gmane-mx.org; Thu, 12 Jan 2023 11:12:08 +0100 Original-Received: by mail-oa1-f63.google.com with SMTP id 586e51a60fabf-15079c0866esf6286115fac.8 for ; Thu, 12 Jan 2023 02:12:08 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=googlegroups.com; s=20210112; h=list-unsubscribe:list-subscribe:list-archive:list-help:list-post :list-id:mailing-list:precedence:reply-to:x-original-sender :mime-version:subject:message-id:to:from:date:sender:from:to:cc :subject:date:message-id:reply-to; bh=v5ePRK6jsquw7i2fSpa/T5tGHdz6rCs22iN3KwNSqw8=; b=NHaCw7e9vFFhpwwuIQOI786AkjlNeBz9qly+SnoXU9psRWqSQkeYIfBY/HOhiZ/isc ee2srKS5ZTXgbNjadNJxPhKoBSACHXEf/oSToZlQ61+F+o+pjQwUAtARMk/CLT5evOXM xUIGfpogIgOjrNVCckdhWt4YCZiuko4UsMd+vY3uNwrXWuBVN7KZA/ckyj1TNbP8FWt9 W6XuB52xVEjmTTJaDn6thldTtk5hVmV0dyTcFqPgacakCyoxBocv8fKD2Xb5yyPEpc+O c8StXUg4EHhCgef5yE/r+NEFav83P9WO/N1bglWCGEf6gFZaP24T3ydMVkXp2TG/MToV H+xg== DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=list-unsubscribe:list-subscribe:list-archive:list-help:list-post :list-id:mailing-list:precedence:reply-to:x-original-sender :mime-version:subject:message-id:to:from:date:from:to:cc:subject :date:message-id:reply-to; bh=v5ePRK6jsquw7i2fSpa/T5tGHdz6rCs22iN3KwNSqw8=; b=RbN2Uo89oyX2pS1eEzayDs/xyE5rGtm/NO6ARhnKU6sjCnnVeAJY6spT+EONj+cGX0 VNZBzE/enXDPN1DZF3inJEcPt3GTVJwSXyW3xkbgSFDL+0mZ6mNter6j8AQIKlUrFcxB VjZHs/KALJGEaN7H6wDTD1Atk74mb7kscdm2wEu3Yckpcw01fWaLmwA7gSLSgObXdnLV UG1Ktue2dFwSR4gFyqFkppw9IUwK3ZdJIpD9V/7M86nTIWBCI7eHa/OIBAMSdN4Yvdfd DEz54LMHHKMwU5KTtCvViTtW7Tf4uOw24pcVkNK+bIENHcIp7/HXWwfwGgKbivRNoovI 8/LQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=list-unsubscribe:list-subscribe:list-archive:list-help:list-post :x-spam-checked-in-group:list-id:mailing-list:precedence:reply-to :x-original-sender:mime-version:subject:message-id:to:from:date :x-gm-message-state:sender:from:to:cc:subject:date:message-id :reply-to; bh=v5ePRK6jsquw7i2fSpa/T5tGHdz6rCs22iN3KwNSqw8=; b=KJgy69hFgKjF3/z8DA+R++WVGuS1ypIuh6ltkiMlfL2oqctosGOxapybX/3vHcDryg Vipb0AgUfAF/Q3qlPfzc6otM8TjW31w+trN8V4a79GNLeX8UyJgscCla3xkif7WQgBqL xhkkkymgAjqtNGGqEp6na2HvMkyn/GFUlnNOT1Cak3IYNkb4osA2H9UFfQeTHlXyBBeM 6i6TJm0RMrTk8Y4R5YI63SJ+IV5ZeeAxyCSIz3g9GSuySeNmov4K25KtQBPQm9Tf77Ud 20Cyo2f/DccSOIWa4uq/KIjIIYsPWPqUAUWb1Wo3dSgCEZGYpzHRIRR+ilKxlWZzaYjN LT8A== Original-Sender: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org X-Gm-Message-State: AFqh2kro6aYkSeHaNgQYDnfZT3+HWrJFW/RwByywkvfOirDh80P/Sxqf ghCZSnEkk1phK01D8xL1WAk= X-Google-Smtp-Source: AMrXdXuTyC8vRTCbiypHH001qCfHzz8t/tF5O+mKIA3KwcVWndY9xBZ91IdtE9pQDombftWEfsN7VQ== X-Received: by 2002:a9d:450a:0:b0:66c:2ffc:392c with SMTP id w10-20020a9d450a000000b0066c2ffc392cmr5242308ote.326.1673518327513; Thu, 12 Jan 2023 02:12:07 -0800 (PST) X-BeenThere: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org Original-Received: by 2002:a05:6870:717:b0:150:4546:6415 with SMTP id ea23-20020a056870071700b0015045466415ls617276oab.11.-pod-prod-gmail; Thu, 12 Jan 2023 02:12:04 -0800 (PST) X-Received: by 2002:a05:6870:aa0e:b0:15b:b9ff:afb8 with SMTP id gv14-20020a056870aa0e00b0015bb9ffafb8mr679317oab.10.1673518324464; Thu, 12 Jan 2023 02:12:04 -0800 (PST) X-Original-Sender: mirp.julia-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org Precedence: list Mailing-list: list pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org; contact pandoc-discuss+owners-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org List-ID: X-Google-Group-Id: 1007024079513 List-Post: , List-Help: , List-Archive: , List-Unsubscribe: , Xref: news.gmane.io gmane.text.pandoc:31979 Archived-At: ------=_Part_4340_1457680069.1673518323762 Content-Type: multipart/alternative; boundary="----=_Part_4341_1071061.1673518323762" ------=_Part_4341_1071061.1673518323762 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi all, I created a mulled biocontainer with pandoc and several R libraries, as it= =20 is a requirement for my R script. But when I try to use it, I get the=20 following error: /usr/local/bin/pandoc: error while loading shared libraries: libgmp.so.10:= =20 cannot open shared object file: No such file or directory=20 204=20 =20 Error in system(paste(shQuote(pandoc_path), "--version"), intern =3D TRUE) = :=20 205=20 =20 error in running command=20 206=20 =20 Calls: ... get_pandoc_version -> with_pandoc_safe_environment= =20 -> force -> system=20 207=20 =20 Execution halted For example, when entering the docker container, I run: docker run -it=20 quay.io/biocontainers/mulled-v2-39480160ac5fd8ae2aaba8eb25795cb6f304e1ca:5e= 51897b0f9cc614dfec8ac1df8b960aeb75dfcd-0=20 bash /usr/local/bin/pandoc and the output is: /usr/local/bin/pandoc: error while loading shared libraries: libgmp.so.10:= =20 cannot open shared object file: No such file or directory I have looked from some solutions, but all of them require installing=20 different pandoc builds ( https://github.com/jgm/pandoc/issues/2774#issuecomment-196380657) or=20 building the binary ( https://github.com/r-hub/rhub-linux-builders/issues/10#issuecomment-2559167= 00),=20 which, as far as I know, is not possible as I need it inside the mulled=20 container which is created automatically. I would appreciate if you can help me solve this problem.=20 Thanks! J=C3=BAlia --=20 You received this message because you are subscribed to the Google Groups "= pandoc-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an e= mail to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To view this discussion on the web visit https://groups.google.com/d/msgid/= pandoc-discuss/b0081f7e-86d7-4025-ae65-561d6871265en%40googlegroups.com. ------=_Part_4341_1071061.1673518323762 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi all,

I created a mulled biocontainer with pandoc an= d several R libraries, as it is a requirement for my R script. But when I t= ry to use it, I get the following error:
/usr/loc= al/bin/pandoc: error while loading shared libraries: libgmp.so.10: cannot o= pen shared object file: No such file or directory
204 Error = in system(paste(shQuote(pandoc_path), "--version"), intern =3D TRUE) :=20
205 erro= r in running command
206 Calls:= <Anonymous> ... get_pandoc_version -> with_pandoc_safe_environmen= t -> force -> system
207 Execut= ion halted

For example,= when entering the docker container, I run:
docker r= un -it quay.io/biocontainers/mulled-v2-39480160ac5fd8ae2aaba8eb25795cb6f304= e1ca:5e51897b0f9cc614dfec8ac1df8b960aeb75dfcd-0 bash
/usr/local/bin/pandoc
and the output is:
/usr/local/bin/pandoc: error while loading shared libraries: li= bgmp.so.10: cannot open shared object file: No such file or directory

I have looked from some solutions, but a= ll of them require installing different pandoc builds (https://github.com= /jgm/pandoc/issues/2774#issuecomment-196380657) or building the binary = (https://github.com/r-hub/rhub-linux-builders/issues/10#issu= ecomment-255916700), which, as far as I know, is not possible as I need= it inside the mulled container which is created automatically.
<= br />
I would appreciate if you can help me solve this problem.= =C2=A0

Thanks!
J=C3=BAlia

--
You received this message because you are subscribed to the Google Groups &= quot;pandoc-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an e= mail to pand= oc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org.
To view this discussion on the web visit https://groups.google.com/d= /msgid/pandoc-discuss/b0081f7e-86d7-4025-ae65-561d6871265en%40googlegroups.= com.
------=_Part_4341_1071061.1673518323762-- ------=_Part_4340_1457680069.1673518323762--