Ari B. Friedman's questions

I am getting the following address when I try building a package in R.

> R CMD build bootLR

...

  cp: error writing '/tmp/RtmpIwkIfV/Rbuild1cf97228aeac/bootLR/.Rproj.user/6295459/sources/s-52F68146/lock_file': Bad address
    ERROR
   copying to build directory failed

Things I have tried:

• Installing Ubuntu 18.04 on a new computer
• Installing Ubuntu 18.04 on a new VM
• Deleting the lock file (it doesn't exist, nor do many of the directories higher than it in the directory heirarchy)
• Googling this error (nothing seems to exist on R specifically; it does seem to be a pointer issue within C perhaps?)
• Waiting 6 months, installing the now-latest R version
• Moving /tmp to a memory disk and rebooting

The best I've gotten it down to is to make the problem intermittent - it built the package once or twice, then started reporting the error again.

To reproduce, install R and all the packages I have installed:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
# Add to /etc/apt/sources.list: deb https://cran.rstudio.com/bin/linux/ubuntu bionic/
sudo apt-get update; sudo apt-get -y install r-base r-base-dev r-recommended libssl-dev libssh2-1-dev
sudo R
install.packages(c("Hmisc","R.utils"))
install.packages(c("RColorBrewer","RCurl","foreign"))
install.packages(c("data.table"))
install.packages(c("tidyverse"))
install.packages(c("functional","XML","MatchIt"))
install.packages(c("taRifx","taRifx.geo","taRifxRcpp","bootLR")) # my packages
install.packages(c("ggplot2","dplyr","stringr", "lubridate","devtools","Roxygen")) # Hadleyverse
install.packages(c("sp","spdep","rgdal","maptools"))
install.packages(c("SDMTools","gstat"))
install.packages(c("automap","RArcInfo","rgeos","spatstat","FNN","fields","MapGAM","spBayes","functional"))
install.packages(c("gtools","gdata","car","formula.tools"))
install.packages(c("testthat","MASS","stargazer","survey","xtable","pander"))
install.packages(c("formatR","caTools","rprojroot","rmarkdown"))
install.packages(c("zeligverse")) 
install.packages(c("boot","binom")) 
install.packages(c("ROAuth","twitteR","RJSONIO")) # webscraping
install.packages(c("pscl","bayesm","perturb","plm"))
install.packages(c("doParallel"))
install.packages(c("HH"))
install.packages(c("equivalence","ROCR","r2stl","svglite"))

Any help/tips you could offer, even as to where I should start looking for the problem, would be most appreciated.

Because laptop screens have gone to ridiculously wide format these days (grumble, grumble, uphill in snow both ways), I'd like to move my XFCE panel to the side rather than the top (i.e. run it vertically). No problem. However, I then want it to run the window switcher icons horizontally.

I can't even locate a set of preferences for what I believe is the Window Switcher plug-in. Some web searches turned up a thread on the Ubuntu Forum about rotating the text in the clock, which would be nice but isn't my primary concern. Really all I care about is the window switchers.

Here's what I have:

Here's what I'd like:

Is this possible?

I want to migrate from Blackberry (RIP). How do I convert my contacts to a standard format?

Possible Duplicate:
What is taking up so much space on my disk, beside the filesystem?

I have a storage drive (2TB) and an OS drive (90GB SSD). I've run out of space on the OS drive:

/$ df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/sdb1        72G   72G     0 100% /
udev            5.9G   12K  5.9G   1% /dev
tmpfs           2.4G  1.2M  2.4G   1% /run
none            5.0M     0  5.0M   0% /run/lock
none            5.9G  428K  5.9G   1% /run/shm
/dev/sda1       1.9T  639G  1.2T  37% /media/StorageDrive

So be it. But when I attempt to figure out where the space has gone, I cannot find it anything remotely approaching the capacity of the drive:

/$ sudo du -h -d 1
du: cannot access `./media/StorageDrive/home/ari/.gvfs': Permission denied
675G    ./media
2.3G    ./var
0   ./proc
7.0M    ./tmp
27M ./boot
4.0K    ./lib64
12K ./dev
44M ./home
16K ./lost+found
8.0M    ./sbin
223M    ./lib
4.0K    ./selinux
1.4M    ./run
140K    ./root
8.8M    ./bin
4.0K    ./mnt
38M ./etc
8.0K    ./srv
4.8G    ./usr
65M ./opt
0   ./sys
682G    .

Note the difference between the total (682G) and the mounted drives in /media (675G) is only about 9G. How are 72G being used? Where is this dark matter hiding?

I've added a bottom taskbar to Unity with tint2. Now I have the taskbar on the bottom of my screen as desired, but when I maximize windows their bottom edge sits under the taskbar that tint2 created.

How do I tell Unity that the bottom X pixels are off-limits?

I moved my home directory to a subdirectory of a second (mounted) drive using usermod -d ... -m. Now, most programs work fine, but a few (Dropbox, etc.) do not. I believe this is because there is no /home/myuser directory any more, so programs that are hard-coded to look there fail.

Can I just create a hard link using ln -d? It seems like hard links are problematic, and I'm not even sure if I can create them across disks anyhow. But I'd like to get this sorted out soon.

I have a bunch of files I want to share on my second internal drive.

I have file sharing off the primary (system) drive working file - Created a samba share user, and I can right-click on the folders I want to share and turn on sharing and it works.

But when I do the same thing off any folder on the secondary drive, it appears to work. Then when I try to access it over the network, the share appears, but upon connecting to the folder I get a message, "The operation can't be completed because the original item for 'ShareName' can't be found." Where 'ShareName' is the name of my share. That is on a OS/X box but I have similar problems when I try accessing it through my BluRay player (which on a previous install of Ubuntu could access the share just fine).

This question seems similar to mine but it has no answers: https://askubuntu.com/questions/111943/sharing-external-drive

I thought maybe it was because the drive was auto-mounted, so I added the following line to my fstab to no avail:

/dev/sda1 /media/StorageDrive ext4 rw,nosuid,nodev,uhelper=udisks 0 0

Then I thought it could be the mount permissions on my second HDD (since I am logging in remotely with an account specifically created for this):

drwx------ 6 mainuser  mainuser  4096 May  6 12:46 StorageDrive

But when I sudo chmod a+r StorageDrive it still doesn't work, despite the permissions changing for that mount session:

drwxr--r-- 6 mainuser  mainuser  4096 May  6 12:46 StorageDrive

Any thoughts?

Requested info

lsblk
NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
sda      8:0    0   1.8T  0 disk 
└─sda1   8:1    0   1.8T  0 part /media/StorageDrive
sr0     11:0    1  1024M  0 rom  
sdb      8:16   0  83.9G  0 disk 
├─sdb1   8:17   0  71.9G  0 part /
├─sdb2   8:18   0     1K  0 part 
└─sdb5   8:21   0    12G  0 part [SWAP]

# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point>   <type>  <options>       <dump>  <pass>
proc            /proc           proc    nodev,noexec,nosuid 0       0
# / was on /dev/sda1 during installation
UUID=4f2a50b6-078a-4a7f-b194-db2f3d66a050 /               ext4    errors=remount-ro,user_xattr 0       1
# swap was on /dev/sda5 during installation
UUID=f7925973-e0e7-4b52-a449-0097230d4aa0 none            swap    sw              0       0
/dev/fd0        /media/floppy0  auto    rw,user,noauto,exec,utf8 0       0

# StorageDrive (UUID so it always identifies the right drive)
UUID="1fe509d8-f4d8-454d-83cc-b74bfb1f1731" /media/StorageDrive ext4 rw,nosuid,nodev,uhelper=udisks,gid=media 0 0

I just upgraded my system and did a clean install of Ubuntu when I did (Installed Oneiric Ocelot from the CD last week but yesterday upgraded to 12.04 LTS). I have an i7 920 (quad core with hyperthreading), so I should be seeing 8 processors, but I only see one in the System Monitor graph.

cat /proc/cpuinfo returns:

processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model       : 26
model name  : Intel(R) Core(TM) i7 CPU         920  @ 2.67GHz
stepping    : 4
microcode   : 0x10
cpu MHz     : 2672.633
cache size  : 8192 KB
physical id : 0
siblings    : 1
core id     : 0
cpu cores   : 1
apicid      : 0
initial apicid  : 0
fpu     : yes
fpu_exception   : yes
cpuid level : 11
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc up arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 popcnt lahf_lm ida dts tpr_shadow vnmi flexpriority ept vpid
bogomips    : 5345.26
clflush size    : 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual
power management:

From my recollection of previous installs with SMP working, there should be multiple entries in /proc/cpuinfo--one per processor. I see only one.

My first thought was that a non-SMP kernel was installed. However, uname -a returns:

Linux compname 3.2.0-24-generic #37-Ubuntu SMP Wed Apr 25 08:43:22 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

So am I using all available cores or not? And if not, what is causing it given that I appear to be running an SMP kernel?

Thanks!