Free Type Error Message

[McCully, Dwayne (NIH/NIAMS) [C]]

Hello UCSC Genome Mirror Support,

 

Some of our users using Firefox, Safari, or Google Chrome are seeing this error when accessing Mouse MM9.

How can I fix this issue?

 

 

 

 

 

Dwayne McCully

SITB, NIAMS, NIH

Contractor

[Maximilian Haeussler]

Hi Dwayne, 

Is freetype-devel installed on your server? It's been a dependency for quite a few years and should be present on almost all linux servers that run anything graphics-related. I am surprised that this is coming up now. 

And because I'm curious for our next release: You're not using our binaries, you're always building from source, right? Can you tell us which linux version you're using?

thanks

Max

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[McCully, Dwayne (NIH/NIAMS) [C]]

Hi Max,

 

The free type development package is installed and I use the browserSetup.sh script to keep my site up to date.

These would be the binaries that are downloaded from your mirror site.

 

BTW:  When I use MS Edge browser I don’t get the error message.  

 

[root@~]# rpm -qa | grep -i freetype

freetype-2.10.4-9.el9.x86_64

freetype-devel-2.10.4-9.el9.x86_64

 

[root@ ~]# more /etc/os-release

NAME="Red Hat Enterprise Linux"

VERSION="9.5 (Plow)"

ID="rhel"

ID_LIKE="fedora"

VERSION_ID="9.5"

PLATFORM_ID="platform:el9"

PRETTY_NAME="Red Hat Enterprise Linux 9.5 (Plow)"

ANSI_COLOR="0;31"

LOGO="fedora-logo-icon"

CPE_NAME="cpe:/o:redhat:enterprise_linux:9::baseos"

HOME_URL=https://www.redhat.com/

DOCUMENTATION_URL=https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/9

BUG_REPORT_URL=https://issues.redhat.com/

 

REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 9"

REDHAT_BUGZILLA_PRODUCT_VERSION=9.5

REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"

REDHAT_SUPPORT_PRODUCT_VERSION="9.5"

 

 

Dwayne

 

Dwayne McCully

NIAMS, NIH

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

 

[Maximilian Haeussler]

Hi Dwayne,

> BTW:  When I use MS Edge browser I don’t get the error message.  

Interesting. This is hard for me to believe, because this error message is output by the CGI program hgTracks if it cannot find the freetype library. Can you confirm that this is true? You can download hgTracks with rsync hgdownload.gi.ucsc.edu::cgi-bin/hgTracks ./, chmod a+x it and then run "ldd", and the program does not even depend on the library as it is statically linked into it. So I guess this error has to do with something else, where somehow the hgTracks program cannot find the font files or something like that?

thanks

Max

[McCully, Dwayne (NIH/NIAMS) [C]]

Hi Max,

 

I don’t get it either as you can see when I use Chrome it does not work but my Edge does work.   Users have seen the same issue on Safari.

 

Google Chrome

 

 

 

 

 

MS Edge

 

[user@ ~]$ ldd hgTracks

        linux-vdso.so.1 (0x00007fff5875b000)

        /lib64/liboneagentproc.so (0x00007efffee00000)

        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007effff19f000)

        libcurl.so.4 => /lib64/libcurl.so.4 (0x00007effff0fd000)

        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007efffea00000)

        libbz2.so.1 => /lib64/libbz2.so.1 (0x00007effff0ea000)

        libdl.so.2 => /lib64/libdl.so.2 (0x00007effff0e3000)

        libm.so.6 => /lib64/libm.so.6 (0x00007efffed25000)

        libz.so.1 => /lib64/libz.so.1 (0x00007effff0c9000)

        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007effff0ae000)

        libc.so.6 => /lib64/libc.so.6 (0x00007efffe600000)

        libnghttp2.so.14 => /lib64/libnghttp2.so.14 (0x00007effff084000)

        libidn2.so.0 => /lib64/libidn2.so.0 (0x00007effff061000)

        libssh.so.4 => /lib64/libssh.so.4 (0x00007efffecb0000)

        libpsl.so.5 => /lib64/libpsl.so.5 (0x00007effff04d000)

        libssl.so.3 => /lib64/libssl.so.3 (0x00007efffe91a000)

        libcrypto.so.3 => /lib64/libcrypto.so.3 (0x00007efffe000000)

        libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00007efffec5a000)

        libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00007efffe840000)

        libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00007effff032000)

        libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00007effff02b000)

        libldap.so.2 => /lib64/libldap.so.2 (0x00007efffe599000)

        liblber.so.2 => /lib64/liblber.so.2 (0x00007efffec48000)

        libbrotlidec.so.1 => /lib64/libbrotlidec.so.1 (0x00007efffec3a000)

        /lib64/ld-linux-x86-64.so.2 (0x00007effff1b1000)

        libunistring.so.2 => /lib64/libunistring.so.2 (0x00007efffde7b000)

        libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00007efffec29000)

        libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00007efffe839000)

        libresolv.so.2 => /lib64/libresolv.so.2 (0x00007efffe825000)

        libevent-2.1.so.7 => /lib64/libevent-2.1.so.7 (0x00007efffe540000)

        libsasl2.so.3 => /lib64/libsasl2.so.3 (0x00007efffe520000)

        libbrotlicommon.so.1 => /lib64/libbrotlicommon.so.1 (0x00007efffde58000)

        libselinux.so.1 => /lib64/libselinux.so.1 (0x00007efffde2b000)

        libcrypt.so.2 => /lib64/libcrypt.so.2 (0x00007efffddf1000)

        libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007efffdd55000)

[Mark Diekhans]

Could you have a different font selected in configure on chrome vs edge?

'McCully, Dwayne (NIH/NIAMS) [C]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu> writes:
> Hi Max,
>
> I don’t get it either as you can see when I use Chrome it does not work but my Edge does work. Users have seen the same issue on Safari.
>
> Google Chrome

> [cid:image0...@01DB614A.9B832920]
>
>
>
>
>
> MS Edge
> [cid:image0...@01DB614A.82B13F90]

> From: Maximilian Haeussler <mhae...@ucsc.edu<mailto:mhae...@ucsc.edu>>
> Sent: Tuesday, January 7, 2025 9:57 AM
> To: McCully, Dwayne (NIH/NIAMS) [C] <dmcc...@mail.nih.gov<mailto:dmcc...@mail.nih.gov>>
> Cc: genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu>; Jung, Seol Kyoung (NIH/NIAMS) [E] <seolkyo...@nih.gov<mailto:seolkyo...@nih.gov>>; Vartak, Supriya (NIH/NIAMS) [E] <supriya...@nih.gov<mailto:supriya...@nih.gov>>
> Subject: [EXTERNAL] Re: [genome-mirror] Free Type Error Message
>
> Hi Dwayne,
>
> Is freetype-devel installed on your server? It's been a dependency for quite a few years and should be present on almost all linux servers that run anything graphics-related. I am surprised that this is coming up now.
>
> And because I'm curious for our next release: You're not using our binaries, you're always building from source, right? Can you tell us which linux version you're using?
>
> thanks
> Max
>

> On Mon, Jan 6, 2025 at 11:47 PM 'McCully, Dwayne (NIH/NIAMS) [C]' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu<mailto:genome...@soe.ucsc.edu>> wrote:
> Hello UCSC Genome Mirror Support,
>
> Some of our users using Firefox, Safari, or Google Chrome are seeing this error when accessing Mouse MM9.
> How can I fix this issue?
>
>
>
>

> [cid:image0...@01DB614A.82B13F90]

>
> Dwayne McCully
> SITB, NIAMS, NIH
> Contractor
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[Maximilian Haeussler]

Mark is right, under Genome Browser > Configuration, you can switch on the old bitmap fonts. Fonts are a user setting. If some internet browsers have cookies or hgsid=xxxx in the URL and these sessions contain settings that switch on the bitmap or vector fonts, then this error will only sometimes come up and not always. 

You can reset a session by going to Genome Browser > Reset all settings for your current internet browser window or opening a new private window. Are the fonts working OK in a new private window? They should always be broken in a new window without cookies, as we default to vector fonts.

You can switch back to the bitmap fonts by clicking Genome Browser > Configure > Fonts = Bitmap or switch them off in hg.conf. This should work around the problem temporarily. 

However, it doesn't address the main question: why are the fonts not working for you. The library is statically built into the binaries. The fonts should be stored at /usr/local/apache/htdocs/urw-fonts/ on your server.

[Brian Raney]

Hello all,

In the screenshot that is working, the fonts being used are the bitmap fonts which don't require the freeType library.  I don't know why the Edge screenshot would be using different fonts, but I'll bet Edge would work if you used them instead of whatever font you have in your session.

In any case, you probably want to use freetype in your build because the fonts are MUCH nicer.

hope this helps,

brian

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[McCully, Dwayne (NIH/NIAMS) [C]]

Hi Mark & Max,

When using Safari or Chrome we will change the font configuration to bitmap to resolve the problem.

Thank's as always for the assistance.

Dwayne

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