The bug
When you are in or above a cloud, you can see through it, but when you are underneath it, you can't. When moving up and down around the cloud level, you can see the blocks behind the clouds appearing and disappearing.
Related issues
is duplicated by
relates to
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Can confirm this. Even with Grafic Settings: Fast (2D clouds) its the same.

yay, so it's not just me ๐

Same problem here.
Reproduced on both windows7 and on linux.
Running unmodified minecraft.jar
Both fast and fancy graphics.

More examples

I agree with this one, because I hate it specially I use beacon to spot my base but the beacon's light always gets cut off because of the clouds since you can't see threw the clouds when you are under it. I wish this will get fixed soon!

Confirmed.

This is most noticeable with the new beacon, if the beam hits the clouds it gets visually "cut off"

Jesper, isn't this related to MC-1398?

@Sid Ben
Ah, yup you're right. I like my description and title more though. Besides, I was first ;p.

Yeah, this report is more detailed

Still confirmed with 1.4.5

Yep, still happening. Also weird to note that at night, if you're lined up right you can still see the moon through the clouds and through whatever blocks the clouds are obscuring.

Duplicate of MC-386.

That is not a duplicate, these are two different issues.

Reopened since another issue as MC-386

Confirmed for 1.4.6 on Linux.

They show the sky behind, you can see start through buildings by looking at clouds at night. 1.4.6
Especially annoying on texture packs with smooth (more transparent) clouds.

Confirmed, still exists in Snapshot 13w04a

Also Snapshot 13w05a and 13w05b
The fix was to revert to how clouds were rendered before beacons. Clouds will now look funny when seen through a beacon beam, but I suppose that's a worthwhile tradeoff to fix this problem.
Reverted this fix because of performance issues. In the future we can fix this again, but with more specific cloud options in the video settings menu.

Did this cause the fps drops? Because I did notice fps drops but my clouds were off.

Rather than in the future, can you do it asap? I'd rather play with low fps but transparent clouds..

An important point. The cloud fix was blamed for the fps drop problem. The fps drop happened in week FIVE, the same week as the stair lighting change. Clouds weren't fixed until week SIX. How are they linked?

That's not it... FPS extremely low because of light. Now I can't play with smooth lighting... It's too laggy. =(

Confirmed for 1.5 ans 13w11a

Confirmed in the just released pre-release for 1.5.1

Confirmed, but only happens for me when im using a hi-res texture pack. Using 1.5.1

I don't know why, but this doesn't happen for me. Clouds are transparent from every direction. I'm playing Minecarft 1.5.2 without any mods.

It only works with blocks, you need to place blocks above the clouds. When you look at the blocks while there's a cloud in front of it, the blocks will disappear. The sun/stars/moon however will still be visible

I know. I tested it with a tower and I can see it from every y level, no matter if I'm above, in or under the clouds.

Do you use any mods?

I have just done some testing, and it seem no matter what i do with optifine adjusting those, it always seems to do this only on my hi resolution texture pack. The only thing that i can find to change it is make the cloud hight higher.

No it is pure vanilla... Weird.

Can confirm this issue with 1.5.2 and 13w18c, regardless of texture pack (default or highres).
@David Lรถffler: Please force a crash by pressing F3 + C for 10 seconds while ingame and attach the crash report here.

Here you go: http://pastebin.com/FwvFcN48
It's weird. I really can see the top half (Edit: From the tower!) from the ground and I have no idea why. I stood right in front of it (Edit: Of the tower!), if that matters (probably not).

Attached crash report to ticket.

you have to be underneath the clouds not right in front of them

Sorry, this wasn't clear. I stood right in front of the tower on the ground. I mean the tower which I can see through the clouds regardless of my Y coordinate. ๐

Confirmed in 13w21a

Still an issue in the 1.6.1 pre-release. Added an image with a donkey.

This is still an issue in the 1.6.1 release, an annoying one at that.

From above: Fine. From within: Fine. From Below: Broken.
Confirmed for 1.6.1 on Linux
$ uname -rms
Linux 3.9.8-1-ARCH x86_64
$ java -version
java version "1.7.0_40"
OpenJDK Runtime Environment (IcedTea 2.4.0) (ArchLinux build 7.u40_2.4.0-1-x86_64)
OpenJDK 64-Bit Server VM (build 24.0-b40, mixed mode)
$ lspci -s 1:00.0
01:00.0 VGA compatible controller: NVIDIA Corporation G94 [GeForce 9600 GT] (rev a1)

Confirmed for 13w36a !

... and 13w36b / 13w37b !

Confirmed for 13w38a/b/c !

Confirmed for 13w39a/b !

I confirm that for 13w39b (And previous), and I have license that 100% Vanilla.

Talven81 what kind of mod are you? Why are you editing comments as you want? Could someone please stop this malicious behavior?

@Dirk Sohler: There was a chain of misunderstandings regarding Launcher versions, that's cleared up now. Please disregard the edits.

Confirmed for 13w41a

Yep, after all the transparency fixes, this still happens.

Confirmed for 13w41b !

Confirmed for 13w42a/b !

Confirmed for 13w43a !

This seems too deliberate to be a bug. Also, Jens commented about a fix in the future. With the new way transparency rendering is handled, is it time to revisit this?

Confirmed for 1.7!

Confirmed for 1.7.1 !

Confirmed for 1.7.2 !

Confirmed for 13w47a/b/c/d/e !

Confirmed for 13w48a/b !

Confirmed for 13w49a

Confirmed for 1.7.3 and 1.7.4

Confirmed for 14w02a/b

Confirmed for 14w04a

Confirmed for 14w06a/b

Confirmed for 14w07a

Confirmed for 14w08a

Confirmed for 1.7.5 and 14w10b

Confirmed for 14w11b

Confirmed for 14w17a

Yup still present in 14w17a

Confirmed for 14w18a

14w19a confirmed

Related: MC-50875
tl:dr It's now happening 1 block too high, so that if your FEET are below the clouds it's not transparent. Supposed to be if your EYES are below the clouds not your feet.

Confirmed for 14w21b.

Confirmed for 14w25b.

A mod was made in 1.7.10 that does fix axactly what is bothering here, maby mojang can add it to the game itselve: http://www.planetminecraft.com/mod/better-clouds/

Present in 1.8-pre1 and pre2.

This will (most likely) be fixed in 1.9:
@TheAkaiyoGaming The cloud rendering code is fricking atrocious and is #1 on my 1.9 hit-list. Until now there was not much to be done.
https://mobile.twitter.com/themogminer/status/507936462827184128

happens in 1.8.1 (release)

Doesn't look like anything was changed for 15w31a. (Ryan Holtz is out of the picture now, so if no work was done after that tweet then who knows if anyone will change it)

there are still a lot of snapshots before the full 1.9 release

Of course there are plenty to come. But the very nature of a bug like this might lend itself to be fixed in the meantime before the snapshots started. Because what has been their focus for these snapshots? Getting new 1.9 features ready to test. Not necessarily browse ancient problems. And what happens when the first snapshot is released? Gotta fix the fresh bugs caused by the new 1.9 features, so that takes time away from the older bugs like this.

Still in 15w38b

Still in 15w43b

Still in 15w44b

Confirmed for:
15w51b
15w51a
15w50a
15w49b
15w47c
15w46a
15w45a

Confirmed for 16w02a.

Affects 16w04a.

Affects 16w05b.

Affects 16w06a.

Affects 16w07a.

Affects 16w07b.

Affects 1.9-pre1.

Affects 1.9-pre3.

Affects 1.9-pre4.

Affects 1.9. ๐

Confirmed for 1.9.1-pre3.

Affects 1.9.2.

Confirmed for 16w15b

Confirmed for 1.9.3-pre3.

Confirmed for 1.9.4.

Confirmed for 16w20a.

Confirmed for 16w21a.

Confirmed for 16w21b.

Confirmed for 1.10-pre1.

Confirmed for 1.10-pre2.

Confirmed for 1.10.

I'm pretty sure the bug is not that clouds are transparent from above, but not from below, but rather that clouds are transparent for everything else than the sky texture (blue at day, black and stars at night, red in between, ...). You can see sun and moon through it and there is no clear border between transparent and opaque.

Confirmed for 1.10.1.

Confirmed for 1.10.2.

@@unknown: 1.10.2 is already marked as affected. In the future, please check the affected versions listed above the description before reconfirming.

Confirmed for 16w41a

Affects 1.13-pre6

Affects 1.13-pre7

Affects 1.13-pre8

Confirmed for 1.13-pre8
[media]@unknown, 1.13-pre8 has already been marked as affected.

Affects 1.13-pre9

Confirmed for 1.13.1.

Affects 19w14a

Affects 19w14b

Works as intended.
@unknown, source?

Still present in 1.14.

Still present in 19w37a.

It's fixed in 19w38b (and I suppose 38a too)
Confirmed to be fixed in 19w38b.

Are they opaque both ways or transparent both ways? I'd assume that the latter would be intended behaviour and the former a bug, and I can't currently test anything right now.
They are now transparent from below, inside, and above.