R `update.packages()` deletes some packages
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It seems that almost every time I run update.packages(), most of the packages are updated, but also a few are removed and not replaced. This time, I copied the activity trail, and after discovering some packages were missing, it appears that those deleted packages correspond to messages like this:
package ‘MASS’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘MASS’
While the message says the package wasn't deleted, it was. Apparently, update.packages() thinks it wasn't, so it doesn't replace it with the new code that it had downloaded.
Losing a sporadic few packages that I thought I was updating is extremely annoying; so I would like to understand what it is that's going wrong so I can avoid it.
I may have a clue about what happens. I use RStudio for most of my work, but I usually bring up a new RGui session and run update.packages() there, so I can keep working while all those updates are being done. Is this likely to be what is causing these deletions? And if so, why?
r package updates
asked Nov 19 at 19:58
rvl
1,7601613
add a comment |
up vote
0
down vote
favorite
It seems that almost every time I run update.packages(), most of the packages are updated, but also a few are removed and not replaced. This time, I copied the activity trail, and after discovering some packages were missing, it appears that those deleted packages correspond to messages like this:
package ‘MASS’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘MASS’
While the message says the package wasn't deleted, it was. Apparently, update.packages() thinks it wasn't, so it doesn't replace it with the new code that it had downloaded.
Losing a sporadic few packages that I thought I was updating is extremely annoying; so I would like to understand what it is that's going wrong so I can avoid it.
I may have a clue about what happens. I use RStudio for most of my work, but I usually bring up a new RGui session and run update.packages() there, so I can keep working while all those updates are being done. Is this likely to be what is causing these deletions? And if so, why?
r package updates
asked Nov 19 at 19:58
rvl
1,7601613
Well, "unpacked" doesn't mean removed. Nothing in that message means that MASS has been removed. Messages like that usually come up for me when I have the package actively loaded when i'm trying to update it and it can't be unloaded because it's being used. It's best to update in a fresh session where you have no packages loaded. It's probably that they aren't deleted, but they may become incompatible with the other versions you have install.
– MrFlick
Nov 19 at 20:07
No. I am not imagining this. The package was actually removed. I can see that by looking st the library directory where the folder no longer exists.
– rvl
Nov 19 at 20:10
I edited the question in an attempt to clarify.
– rvl
Nov 19 at 20:49
add a comment |
up vote
0
down vote
favorite
up vote
0
down vote
favorite
It seems that almost every time I run update.packages(), most of the packages are updated, but also a few are removed and not replaced. This time, I copied the activity trail, and after discovering some packages were missing, it appears that those deleted packages correspond to messages like this:
package ‘MASS’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘MASS’
While the message says the package wasn't deleted, it was. Apparently, update.packages() thinks it wasn't, so it doesn't replace it with the new code that it had downloaded.
Losing a sporadic few packages that I thought I was updating is extremely annoying; so I would like to understand what it is that's going wrong so I can avoid it.
I may have a clue about what happens. I use RStudio for most of my work, but I usually bring up a new RGui session and run update.packages() there, so I can keep working while all those updates are being done. Is this likely to be what is causing these deletions? And if so, why?
r package updates
asked Nov 19 at 19:58
rvl
1,7601613
It seems that almost every time I run update.packages(), most of the packages are updated, but also a few are removed and not replaced. This time, I copied the activity trail, and after discovering some packages were missing, it appears that those deleted packages correspond to messages like this:
package ‘MASS’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘MASS’
While the message says the package wasn't deleted, it was. Apparently, update.packages() thinks it wasn't, so it doesn't replace it with the new code that it had downloaded.
Losing a sporadic few packages that I thought I was updating is extremely annoying; so I would like to understand what it is that's going wrong so I can avoid it.
I may have a clue about what happens. I use RStudio for most of my work, but I usually bring up a new RGui session and run update.packages() there, so I can keep working while all those updates are being done. Is this likely to be what is causing these deletions? And if so, why?
r package updates
r package updates
asked Nov 19 at 19:58
rvl
1,7601613
asked Nov 19 at 19:58
rvl
1,7601613
edited Nov 19 at 20:43
asked Nov 19 at 19:58
rvl
1,7601613
asked Nov 19 at 19:58
rvl
1,7601613
asked Nov 19 at 19:58
rvl
1,7601613
1,7601613
Well, "unpacked" doesn't mean removed. Nothing in that message means that MASS has been removed. Messages like that usually come up for me when I have the package actively loaded when i'm trying to update it and it can't be unloaded because it's being used. It's best to update in a fresh session where you have no packages loaded. It's probably that they aren't deleted, but they may become incompatible with the other versions you have install.
– MrFlick
Nov 19 at 20:07
No. I am not imagining this. The package was actually removed. I can see that by looking st the library directory where the folder no longer exists.
– rvl
Nov 19 at 20:10
I edited the question in an attempt to clarify.
– rvl
Nov 19 at 20:49
add a comment |
Well, "unpacked" doesn't mean removed. Nothing in that message means that MASS has been removed. Messages like that usually come up for me when I have the package actively loaded when i'm trying to update it and it can't be unloaded because it's being used. It's best to update in a fresh session where you have no packages loaded. It's probably that they aren't deleted, but they may become incompatible with the other versions you have install.
– MrFlick
Nov 19 at 20:07
No. I am not imagining this. The package was actually removed. I can see that by looking st the library directory where the folder no longer exists.
– rvl
Nov 19 at 20:10
I edited the question in an attempt to clarify.
– rvl
Nov 19 at 20:49
Well, "unpacked" doesn't mean removed. Nothing in that message means that MASS has been removed. Messages like that usually come up for me when I have the package actively loaded when i'm trying to update it and it can't be unloaded because it's being used. It's best to update in a fresh session where you have no packages loaded. It's probably that they aren't deleted, but they may become incompatible with the other versions you have install.
– MrFlick
Nov 19 at 20:07
Well, "unpacked" doesn't mean removed. Nothing in that message means that MASS has been removed. Messages like that usually come up for me when I have the package actively loaded when i'm trying to update it and it can't be unloaded because it's being used. It's best to update in a fresh session where you have no packages loaded. It's probably that they aren't deleted, but they may become incompatible with the other versions you have install.
– MrFlick
Nov 19 at 20:07
No. I am not imagining this. The package was actually removed. I can see that by looking st the library directory where the folder no longer exists.
– rvl
Nov 19 at 20:10
No. I am not imagining this. The package was actually removed. I can see that by looking st the library directory where the folder no longer exists.
– rvl
Nov 19 at 20:10
I edited the question in an attempt to clarify.
– rvl
Nov 19 at 20:49
I edited the question in an attempt to clarify.
– rvl
Nov 19 at 20:49
add a comment |
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Well, "unpacked" doesn't mean removed. Nothing in that message means that MASS has been removed. Messages like that usually come up for me when I have the package actively loaded when i'm trying to update it and it can't be unloaded because it's being used. It's best to update in a fresh session where you have no packages loaded. It's probably that they aren't deleted, but they may become incompatible with the other versions you have install.
– MrFlick
Nov 19 at 20:07
No. I am not imagining this. The package was actually removed. I can see that by looking st the library directory where the folder no longer exists.
– rvl
Nov 19 at 20:10
I edited the question in an attempt to clarify.
– rvl
Nov 19 at 20:49