Higher number of files and lower bytes sync-ed in destination folder?

Hi,
I was wondering if this issue is already known or has an explanation / solution? Strangely if I copy + paste, it works fine. But if I use rsync it shows a different number of files and bytes. I noticed there are some 'icon?' files in some of the directories which might explain the additional files (?), but I don't understand how the file size total can be 15% lower than it should be. It doesn't happen to all folders/files, but it is affecting more than one folder/file.

Thanks,
Tom

Hi @curioustom20,
It pretty much depends on the setup you use during syncing. rsync alone has many different switches and options on how to synchronise the selected source, differing in symlinks handling, do-not-delete in target, only newer, etc. so there's definitely no universal hint to give here.
I use the default settings to perform my personal backups, which are (at least in my conditions) somehow 1:1 as I need. Toggling the switches can quickly differ the result in some way. 🤔
If you could provide the final rsync command (can be read at the top of the Output even when running a Simulated run) along with some basic knowledge about what's missing and what's redundant in the target folder, I could give it a deeper look.

Hi @username0x0a,
Many thanks for the quick reply - yes, I did do a few attempts (of the same folder) with different settings but it didn't seem to change anything. I've done it again with this (I think the default) rsync command:
/usr/bin/rsync -t -p -o -g -E --delete -v --progress -l -i -r -n /Users/tgc/Dropbox /Volumes/macmini/Desktop/MB Air backup
Destination folder differences

Strangely, there should be 44.1mb less in the destination folder, but when digging into where these mb are missing, I can only see 6.1mb if comparing all 4 folders. There are also 5 files at root level BUT no file size differences between origin and destination folders. Only other difference is the 0-byte 'Icon?' file... So where did the other missing 38mb go?! Could it be that this 'Icon?' file is changing how the files / folders are being scanned/read? (Sorry, not a techie! Just brainstorming)

'Icon?' file (0 bytes) in multiple but not all folders

I spotted one temporary file of another existing permanent file ('~$Stanton tasks.xlsx') but very low in bytes (171bytes vs. 61kb for the permanent file). This file wasn't open, so not sure why there is a temp file.

There is no trend of which files are smaller in size, but some (not all) png and psd files. Interestingly, they DO open without error despite the lower file size - it's almost like it's been compressed, although this option was not clicked on the Advanced tab?

P.S. The output of the rysnc:
/usr/bin/rsync -t -p -o -g -E --delete -v --progress -l -i -r /Users/tgc/Dropbox /Volumes/macmini/Desktop/MB Air backup
building file list ...
0 files...
600 files...
612 files to consider
cd+++++++ Dropbox/
send_files failed to open "/tmp/.._Dropbox.QMFNjI": Operation not permitted

f+++++++ Dropbox/.DS_Store
14340 100%    0.00kB/s    0:00:00
14340 100%    0.00kB/s    0:00:00 (xfer#2, to-check=609/612)
send_files failed to open "/tmp/...DS_Store.gOml4m": Operation not permitted
cd+++++++ Dropbox/.dropbox.cache/
send_files failed to open "/tmp/...dropbox.cache.3o2ymA": Operation not permitted
cd+++++++ Dropbox/Applications - 2020/
send_files failed to open "/tmp/.._Applications - 2020.xpZn7B": Operation not permitted
cd+++++++ Dropbox/Carlos/
send_files failed to open "/tmp/.._Carlos.nfmLi3": Operation not permitted
f+++++++ Dropbox/Certified Passport - Tim Crouch - 27 Oct 2020.jpg
32768   1%  351.65kB/s    0:00:08
3135233 100%    6.18MB/s    0:00:00 (xfer#7, to-check=595/612)
send_files failed to open "/tmp/.._Certified Passport - Tim Crouch - 27 Oct 2020.jpg.2zQiPZ": Operation not permitted
f+++++++ Dropbox/Content site analysis - May 2020.xlsx
32768  68%   51.28kB/s    0:00:00
47592 100%   74.36kB/s    0:00:00 (xfer#9, to-check=594/612)
send_files failed to open "/tmp/.._Content site analysis - May 2020.xlsx.8683Lp": Operation not permitted
f+++++++ Dropbox/HMRC Appeal Letter.docx
32768  30%   43.54kB/s    0:00:01
107864 100%  143.12kB/s    0:00:00 (xfer#11, to-check=593/612)
send_files failed to open "/tmp/.._HMRC Appeal Letter.docx.XAZMiJ": Operation not permitted
f+++++++ Dropbox/Icon#015
0 100%    0.00kB/s    0:00:00 (xfer#13, to-check=592/612)
send_files failed to open "/tmp/.._Icon#015.cEtV9Q": Operation not permitted
cd+++++++ Dropbox/Intent Payslips/
send_files failed to open "/tmp/.._Intent Payslips.TbTZFl": Operation not permitted
f+++++++ Dropbox/Intent sales pitch v3.docx
32768  25%   31.56kB/s    0:00:03
65536  50%   63.12kB/s    0:00:01
129751 100%  124.84kB/s    0:00:01 (xfer#16, to-check=591/612)
send_files failed to open "/tmp/.._Intent sales pitch v3.docx.xvES2P": Operation not permitted
f+++++++ Dropbox/SM-Easiest-Passport-Comparison-Sheet.pdf
32768   3%  193.94kB/s    0:00:04
895926 100%    1.74MB/s    0:00:00 (xfer#18, to-check=590/612)
send_files failed to open "/tmp/.._SM-Easiest-Passport-Comparison-Sheet.pdf.qd1Ozx": Operation not permitted
cd+++++++ Dropbox/Stanton House/
send_files failed to open "/tmp/.._Stanton House.Luq7t2": Operation not permitted
f+++++++ Dropbox/.dropbox
41 100%    0.08kB/s    0:00:00
41 100%    0.08kB/s    0:00:00 (xfer#21, to-check=596/612)
cd+++++++ Dropbox/.dropbox.cache/attrs_cache/
cd+++++++ Dropbox/.dropbox.cache/icons/
f+++++++ Dropbox/.dropbox.cache/icons/CameraUploads
0 100%    0.00kB/s    0:00:00 (xfer#22, to-check=566/612)
send_files failed to open "/tmp/.._CameraUploads.m0f69J": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderDesktop
0 100%    0.00kB/s    0:00:00 (xfer#24, to-check=565/612)
send_files failed to open "/tmp/.._DeviceFolderDesktop.8DuAr6": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderDocuments
0 100%    0.00kB/s    0:00:00 (xfer#26, to-check=564/612)
send_files failed to open "/tmp/.._DeviceFolderDocuments.ZEsj8Z": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderDownloads
0 100%    0.00kB/s    0:00:00 (xfer#28, to-check=563/612)
send_files failed to open "/tmp/.._DeviceFolderDownloads.z2gzdU": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderGeneric
0 100%    0.00kB/s    0:00:00 (xfer#30, to-check=562/612)
send_files failed to open "/tmp/.._DeviceFolderGeneric.NjiAFa": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderMac
0 100%    0.00kB/s    0:00:00 (xfer#32, to-check=561/612)
send_files failed to open "/tmp/.._DeviceFolderMac.10pPOT": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderMusic
0 100%    0.00kB/s    0:00:00 (xfer#34, to-check=560/612)
send_files failed to open "/tmp/.._DeviceFolderMusic.bpq3gE": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderPictures
0 100%    0.00kB/s    0:00:00 (xfer#36, to-check=559/612)
send_files failed to open "/tmp/.._DeviceFolderPictures.4rkYLU": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderVideos
0 100%    0.00kB/s    0:00:00 (xfer#38, to-check=558/612)
send_files failed to open "/tmp/.._DeviceFolderVideos.bTaSAc": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DeviceFolderWin
0 100%    0.00kB/s    0:00:00 (xfer#40, to-check=557/612)
send_files failed to open "/tmp/.._DeviceFolderWin.hfvBw3": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/DropboxFolder
0 100%    0.00kB/s    0:00:00 (xfer#42, to-check=556/612)
send_files failed to open "/tmp/.._DropboxFolder.VdpG5P": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/FamilySharedFolder
0 100%    0.00kB/s    0:00:00 (xfer#44, to-check=555/612)
send_files failed to open "/tmp/.._FamilySharedFolder.kbZ5aE": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/Sandbox
0 100%    0.00kB/s    0:00:00 (xfer#46, to-check=554/612)
send_files failed to open "/tmp/.._Sandbox.T0LmZk": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/Shared
0 100%    0.00kB/s    0:00:00 (xfer#48, to-check=553/612)
send_files failed to open "/tmp/.._Shared.8rCOCK": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/SharedReadOnly
0 100%    0.00kB/s    0:00:00 (xfer#50, to-check=552/612)
send_files failed to open "/tmp/.._SharedReadOnly.WbSPH7": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/SharedViewNameOnly
0 100%    0.00kB/s    0:00:00 (xfer#52, to-check=551/612)
send_files failed to open "/tmp/.._SharedViewNameOnly.qldMxl": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/TeamFolder
0 100%    0.00kB/s    0:00:00 (xfer#54, to-check=550/612)
send_files failed to open "/tmp/.._TeamFolder.ogpJXf": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/TeamFolderReadOnly
0 100%    0.00kB/s    0:00:00 (xfer#56, to-check=549/612)
send_files failed to open "/tmp/.._TeamFolderReadOnly.HIvqWG": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/TeamMemberFolder
0 100%    0.00kB/s    0:00:00 (xfer#58, to-check=548/612)
send_files failed to open "/tmp/.._TeamMemberFolder.wyP03j": Operation not permitted
f+++++++ Dropbox/.dropbox.cache/icons/Vault
0 100%    0.00kB/s    0:00:00 (xfer#60, to-check=547/612)
send_files failed to open "/tmp/..Vault.IxM3bG": Operation not permitted
cd+++++++ Dropbox/.dropbox.cache/new_files/
cd+++++++ Dropbox/.dropbox.cache/old_files/
cd+++++++ Dropbox/.dropbox.cache/placeholder_cache/
cd+++++++ Dropbox/.dropbox.cache/prefetch_cache/
cd+++++++ Dropbox/.dropbox.cache/tmp_dirs/
f+++++++ Dropbox/Applications - 2020/.DS_Store
8196 100%   14.69kB/s    0:00:00
8196 100%   14.69kB/s    0:00:00 (xfer#62, to-check=540/612)
send_files failed to open "/tmp/...DS_Store.JlQoX9": Operation not permitted
cd+++++++ Dropbox/Applications - 2020/CV Strategic Accounts/
send_files failed to open "/tmp/.._CV Strategic Accounts.n29K1c": Operation not permitted
cd+++++++ Dropbox/Applications - 2020/CV Strategic Partnerships/
send_files failed to open "/tmp/.._CV Strategic Partnerships.8rNHIo": Operation not permitted
cd+++++++ Dropbox/Applications - 2020/CV Strategic Sales/
send_files failed to open "/tmp/.._CV Strategic Sales.lqZ1Qi": Operation not permitted
f+++++++ Dropbox/Applications - 2020/Job applications Oct 2020.xlsx
25465 100%    0.00kB/s    0:00:00
25465 100%    0.00kB/s    0:00:00 (xfer#67, to-check=531/612)
send_files failed to open "/tmp/.._Job applications Oct 2020.xlsx.jSpjO9": Operation not permitted
f+++++++ Dropbox/Applications - 2020/Tim Crouch CV Nov 2020.docx
32768  16%  307.69kB/s    0:00:00
194050 100%    1.76MB/s    0:00:00 (xfer#69, to-check=530/612)
send_files failed to open "/tmp/.._Tim Crouch CV Nov 2020.docx.Ydil5T": Operation not permitted
f+++++++ Dropbox/Applications - 2020/Tim Crouch CV Oct 2020 OLD.docx
32768  17%  125.00kB/s    0:00:01
182831 100%  694.73kB/s    0:00:00 (xfer#71, to-check=529/612)
send_files failed to open "/tmp/.._Tim Crouch CV Oct 2020 OLD.docx.BpPZfa": Operation not permitted
cd+++++++ Dropbox/Applications - 2020/Uber Head of Strategic Partnerships ANZ/
send_files failed to open "/tmp/.._Uber Head of Strategic Partnerships ANZ.dlZcPE": Operation not permitted
f+++++++ Dropbox/Applications - 2020/CV Strategic Accounts/Tim Crouch CV Jan 2021.pdf
32768  29%   63.87kB/s    0:00:01
111851 100%  218.02kB/s    0:00:00 (xfer#74, to-check=525/612)
send_files failed to open "/tmp/.._Tim Crouch CV Jan 2021.pdf.f9gGm8": Operation not permitted
f+++++++ Dropbox/Applications - 2020/CV Strategic Accounts/Tim Crouch CV Nov 2020.pdf
32768  29%   47.98kB/s    0:00:01
111486 100%  163.23kB/s    0:00:00 (xfer#76, to-check=524/612)
send_files failed to open "/tmp/.._Tim Crouch CV Nov 2020.pdf.96zytk": Operation not permitted
f+++++++ Dropbox/Applications - 2020/CV Strategic Partnerships/Tim Crouch CV Dec 2020.pdf
32768  29%   38.74kB/s    0:00:02
111918 100%  132.32kB/s    0:00:00 (xfer#78, to-check=519/612)
send_files failed to open "/tmp/.._Tim Crouch CV Dec 2020.pdf.32weL9": Operation not permitted
f+++++++ Dropbox/Applications - 2020/CV Strategic Partnerships/Tim Crouch CV Jan 2021.pdf
32768  29%   33.37kB/s    0:00:02
111941 100%  113.99kB/s    0:00:00 (xfer#80, to-check=518/612)
send_files failed to open "/tmp/.._Tim Crouch CV Jan 2021.pdf.Bbzcs0": Operation not permitted
f+++++++ Dropbox/Applications - 2020/CV Strategic Partnerships/Tim Crouch CV Nov 2020.pdf
32768  29%   28.99kB/s    0:00:02
65536  58%   57.97kB/s    0:00:00
111479 100%   98.52kB/s    0:00:01 (xfer#82, to-check=517/612)
send_files failed to open "/tmp/.._Tim Crouch CV Nov 2020.pdf.14VUm0": Operation not permitted
f+++++++ Dropbox/Applications - 2020/CV Strategic Sales/Tim Crouch CV Jan 2021.pdf
32768  29%   32.23kB/s    0:00:02
111822 100%  109.97kB/s    0:00:00 (xfer#84, to-check=513/612)
send_files failed to open "/tmp/.._Tim Crouch CV Jan 2021.pdf.lD0vXm": Operation not permitted
f+++++++ Dropbox/Applications - 2020/CV Strategic Sales/Tim Crouch CV Nov 2020.pdf
32768  29%    0.00kB/s    0:00:00
111506 100%   75.09MB/s    0:00:00 (xfer#86, to-check=512/612)
send_files failed to open "/tmp/.._Tim Crouch CV Nov 2020.pdf.8vcEuM": Operation not permitted
f+++++++ Dropbox/Applications - 2020/Uber Head of Strategic Partnerships ANZ/Workbook1.xlsx
30558 100%   37.77kB/s    0:00:00
30558 100%   37.77kB/s    0:00:00 (xfer#88, to-check=509/612)
send_files failed to open "/tmp/..Workbook1.xlsx.HX9En2": Operation not permitted
f+++++++ Dropbox/Carlos/.DS_Store
14340 100%   15.79kB/s    0:00:00
14340 100%   15.79kB/s    0:00:00 (xfer#90, to-check=507/612)
send_files failed to open "/tmp/...DS_Store.uKUYrT": Operation not permitted
cd+++++++ Dropbox/Carlos/Escape Projects/
send_files failed to open "/tmp/.._Escape Projects.vCwxx5": Operation not permitted
f+++++++ Dropbox/Carlos/Icon#015
0 100%    0.00kB/s    0:00:00 (xfer#93, to-check=501/612)
send_files failed to open "/tmp/.._Icon#015.FLa2oe": Operation not permitted
cd+++++++ Dropbox/Carlos/Ideas/
send_files failed to open "/tmp/.._Ideas.l3bziS": Operation not permitted
cd+++++++ Dropbox/Carlos/Toy Dropshipping/
send_files failed to open "/tmp/..Toy Dropshipping.T1SHbP": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/.DS_Store
8196 100%    8.97kB/s    0:00:00
8196 100%    8.96kB/s    0:00:00 (xfer#97, to-check=499/612)
send_files failed to open "/tmp/...DS_Store.yOqikW": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Archive - 1 Fred's Place - Launch Open Day- Eventbrite.pdf
32768   2%   26.32kB/s    0:00:50
65536   4%   52.63kB/s    0:00:24
1352306 100%  910.77kB/s    0:00:01 (xfer#99, to-check=485/612)
send_files failed to open "/tmp/.._Archive - 1 Fred's Place - Launch Open Day- Eventbrite.pdf.dUKKyF": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Draft - Mailshot TC.docx
32768  41%   98.46kB/s    0:00:00
79791 100%  239.02kB/s    0:00:00 (xfer#101, to-check=484/612)
send_files failed to open "/tmp/.._Draft - Mailshot TC.docx.7wF14B": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/EP - Organisations Directory.xlsx
32768  72%   74.94kB/s    0:00:00
45200 100%  103.37kB/s    0:00:00 (xfer#103, to-check=483/612)
send_files failed to open "/tmp/.._EP - Organisations Directory.xlsx.trKTP7": Operation not permitted
cd+++++++ Dropbox/Carlos/Escape Projects/Graphics/
send_files failed to open "/tmp/.._Graphics.2fas79": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Incubators mail draft TC.docx
32768  38%   55.27kB/s    0:00:00
84113 100%  141.62kB/s    0:00:00 (xfer#106, to-check=482/612)
send_files failed to open "/tmp/.._Incubators mail draft TC.docx.gLOdnz": Operation not permitted
cd+++++++ Dropbox/Carlos/Escape Projects/PR/
send_files failed to open "/tmp/.._PR.L0WDZw": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Site Logo EP TC.psd
32768   4%   46.85kB/s    0:00:15
769512 100%  978.49kB/s    0:00:00 (xfer#109, to-check=481/612)
send_files failed to open "/tmp/.._Site Logo EP TC.psd.YXD04y": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Social Media - Post Records.xlsx
32768  60%   35.75kB/s    0:00:00
53792 100%   58.69kB/s    0:00:00 (xfer#111, to-check=480/612)
send_files failed to open "/tmp/.._Social Media - Post Records.xlsx.g0qtz1": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Start-ups mail draft TC.docx
32768  40%   32.62kB/s    0:00:01
80042 100%   79.68kB/s    0:00:00 (xfer#113, to-check=479/612)
send_files failed to open "/tmp/.._Start-ups mail draft TC.docx.XQU3Ak": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/To do.xlsx
32768  75%   28.93kB/s    0:00:00
43181 100%   38.13kB/s    0:00:00
43181 100%   38.13kB/s    0:00:01 (xfer#115, to-check=478/612)
send_files failed to open "/tmp/.._To do.xlsx.u8GiMl": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Unpaid internship rules.pdf
32768  28%  372.09kB/s    0:00:00
115660 100%    1.27MB/s    0:00:00 (xfer#117, to-check=477/612)
send_files failed to open "/tmp/.._Unpaid internship rules.pdf.lYQ4OT": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Workbook3.xlsx
26522 100%  139.25kB/s    0:00:00
26522 100%  139.25kB/s    0:00:00 (xfer#119, to-check=476/612)
send_files failed to open "/tmp/..Workbook3.xlsx.4NN05Q": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/.DS_Store
8196 100%   41.91kB/s    0:00:00
8196 100%   41.91kB/s    0:00:00 (xfer#121, to-check=474/612)
send_files failed to open "/tmp/...DS_Store.23jVSy": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/Business Card Template Side 2.psd
32768   2%   66.53kB/s    0:00:23
1081344  68%  942.86kB/s    0:00:00
1581528 100%    1.13MB/s    0:00:01 (xfer#123, to-check=436/612)
send_files failed to open "/tmp/.._Business Card Template Side 2.psd.QNzAf3": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/Business Card Template Side 3-Back-CARLOS.psd
32768   1%   89.89kB/s    0:00:21
1867776  94%    1.76MB/s    0:00:00
1974813 100%    1.86MB/s    0:00:01 (xfer#125, to-check=435/612)
send_files failed to open "/tmp/.._Business Card Template Side 3-Back-CARLOS.psd.2rUSzn": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/Business Card Template Side 3-Back.psd
32768   1%  179.78kB/s    0:00:10
1971203 100%    2.13MB/s    0:00:00 (xfer#127, to-check=434/612)
send_files failed to open "/tmp/.._Business Card Template Side 3-Back.psd.FOzV9r": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/Business Card Template Side 3-Recovered.psd
32768   2%   29.52kB/s    0:00:45
65536   4%   59.04kB/s    0:00:22
1373179 100%  836.03kB/s    0:00:01 (xfer#129, to-check=433/612)
send_files failed to open "/tmp/.._Business Card Template Side 3-Recovered.psd.YIsfEW": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/Business Card Template Side 3.psd
32768   2%   47.27kB/s    0:00:31
557056  36%  520.08kB/s    0:00:01
1539319 100%    1.09MB/s    0:00:01 (xfer#131, to-check=432/612)
send_files failed to open "/tmp/.._Business Card Template Side 3.psd.zMEjpX": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/Business Card Template.psd
32768   2%   55.75kB/s    0:00:28
1081344  66% 1023.26kB/s    0:00:00
1623184 100%    1.03MB/s    0:00:01 (xfer#133, to-check=431/612)
send_files failed to open "/tmp/.._Business Card Template.psd.4GcY3s": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/Business-Card-Template-Side-1.png
32768  58%   42.84kB/s    0:00:00
56152 100%   73.41kB/s    0:00:00 (xfer#135, to-check=430/612)
send_files failed to open "/tmp/.._Business-Card-Template-Side-1.png.vYmZC8": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/Business-Card-Template-Side-3.png
32768  68%   35.20kB/s    0:00:00
47741 100%   51.29kB/s    0:00:00 (xfer#137, to-check=429/612)
send_files failed to open "/tmp/.._Business-Card-Template-Side-3.png.QWyIbl": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/BusinessCardBackCarlos.png
32768  40%   31.40kB/s    0:00:01
65536  80%   62.81kB/s    0:00:00
81800 100%   78.39kB/s    0:00:01 (xfer#139, to-check=428/612)
send_files failed to open "/tmp/.._BusinessCardBackCarlos.png.eIDcor": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/BusinessCardBackTim.png
32768  41%  271.19kB/s    0:00:00
79733 100%  659.87kB/s    0:00:00 (xfer#141, to-check=427/612)
send_files failed to open "/tmp/.._BusinessCardBackTim.png.6drrCX": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/BusinessCardFront.png
32768  89%  125.49kB/s    0:00:00
36697 100%  140.54kB/s    0:00:00 (xfer#143, to-check=426/612)
send_files failed to open "/tmp/.._BusinessCardFront.png.3LhY8T": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/EP Logo MAILCHIMP.psd
32768  18%   86.72kB/s    0:00:01
178468 100%  471.04kB/s    0:00:00 (xfer#145, to-check=425/612)
send_files failed to open "/tmp/.._EP Logo MAILCHIMP.psd.yP3O4w": Operation not permitted
f+++++++ Dropbox/Carlos/Escape Projects/Graphics/EP Logo TC.png
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f+++++++ Dropbox/Stanton House/Stanton tasks.xlsx
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f+++++++ Dropbox/Stanton House/~$Stanton tasks.xlsx
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f+++++++ Dropbox/Stanton House/Cutty Sark Flat Prices/Delaney House 2bed 360k SOLD.pdf
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f+++++++ Dropbox/Stanton House/Cutty Sark Flat Prices/Delaney House 2bed 375k.pdf
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f+++++++ Dropbox/Stanton House/Cutty Sark Flat Prices/Haddo St 3bed 350k.pdf
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f+++++++ Dropbox/Stanton House/Cutty Sark Flat Prices/Macey House 2bed 385k.pdf
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f+++++++ Dropbox/Stanton House/Cutty Sark Flat Prices/Rockfield House 1bed 315k.pdf
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f+++++++ Dropbox/Stanton House/Cutty Sark Flat Prices/Rockfield House 3bed 405k.pdf
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f+++++++ Dropbox/Stanton House/Cutty Sark Flat Prices/Thames St 3 bed 365k.pdf
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f+++++++ Dropbox/Stanton House/Gas Safety Certificates/Gas Safety Certificate - 20 Jan 2018.jpg
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f+++++++ Dropbox/Stanton House/Gas Safety Certificates/GasCert-103324769.pdf
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f+++++++ Dropbox/Stanton House/HMO Application/.DS_Store
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f+++++++ Dropbox/Stanton House/HMO Application/5 Nov 2014 - Electricity Rewiring Certificate.pdf
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send_files failed to open "/tmp/.._5 Nov 2014 - Electricity Rewiring Certificate.pdf.ft9Nsd": Operation not permitted
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f+++++++ Dropbox/Stanton House/HMO Application/HMO Application Fee - Admin Fee part.png
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f+++++++ Dropbox/Stanton House/HMO Application/HMO_Minumum_Standards_2017.pdf
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f+++++++ Dropbox/Stanton House/HMO Application/Holding document.docx
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f+++++++ Dropbox/Stanton House/HMO Application/Stanton House Floorplan - Mar 2018.jpg
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f+++++++ Dropbox/Stanton House/HMO Application/Tim Crouch - Basic DBS Check - HMO Application - 3 Mar 2018.png
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f+++++++ Dropbox/Stanton House/Howsy/.DS_Store
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send_files failed to open "/tmp/...DS_Store.JBvnKW": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Contracts/
send_files failed to open "/tmp/.._Contracts.i0OAwd": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Faith Williams.pdf
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send_files failed to open "/tmp/.._Faith Williams.pdf.C7TYFU": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/ID/
send_files failed to open "/tmp/.._ID.QUiyIG": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Photos/
send_files failed to open "/tmp/.._Photos.M66OsJ": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Property Documents/
send_files failed to open "/tmp/..Property Documents.aGZxJ5": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/.DS_Store
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send_files failed to open "/tmp/...DS_Store.xqkYhd": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/
send_files failed to open "/tmp/.._ARCHIVED.w5hNGx": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Contracts/Chloe Ryan/
send_files failed to open "/tmp/.._Chloe Ryan.Rcf74M": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Contracts/Elena Cami/
send_files failed to open "/tmp/.._Elena Cami.wgThbd": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/Faith Williams Passport.jpg
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f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/.DS_Store
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f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/AST - Bridget Gaskell - 1 Dec 2018.pdf
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send_files failed to open "/tmp/.._AST - Bridget Gaskell - 1 Dec 2018.pdf.dWY9Rb": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/AST Agreement - Michael Beskine - Jul2019.pdf
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f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Domenico Curigliano - Tenancy Agreement 15 April 2018.pdf
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f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Joe Cooper Tenancy Agreement 1 Nov 2017.pdf
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f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Michael Beskine - 8 July 2019.jpg
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send_files failed to open "/tmp/.._Michael Beskine - 8 July 2019.jpg.k63U11": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Michael Beskine AST - 8 July 2019.pdf
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send_files failed to open "/tmp/.._Michael Beskine AST - 8 July 2019.pdf.ID8mrX": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Raphaelle Masquillier/
send_files failed to open "/tmp/.._Raphaelle Masquillier.S93ooC": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Ruby Molyneux/
send_files failed to open "/tmp/..Ruby Molyneux.Vf1eUh": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Raphaelle Masquillier/.DS_Store
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send_files failed to open "/tmp/...DS_Store.nd0X8j": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Raphaelle Masquillier/AST Raphaelle Masquillier.pdf
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send_files failed to open "/tmp/.._AST Raphaelle Masquillier.pdf.hEdNJX": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Raphaelle Masquillier/DPS Raphaelle Masquillier.pdf
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send_files failed to open "/tmp/.._DPS Raphaelle Masquillier.pdf.7dikQS": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Raphaelle Masquillier/Raphaelle Masquillier - Signed Contract (3 Jun 2018) and Work Contract.pdf
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send_files failed to open "/tmp/.._Raphaelle Masquillier - Signed Contract (3 Jun 2018) and Work Contract.pdf.s6nMLx": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Raphaelle Masquillier/Raphaelle Masquillier Passport.jpeg
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send_files failed to open "/tmp/..Raphaelle Masquillier Passport.jpeg.RoLGaL": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Ruby Molyneux/.DS_Store
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6148 100%    7.86kB/s    0:00:00 (xfer#362, to-check=218/612)
send_files failed to open "/tmp/...DS_Store.RcLOqM": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Ruby Molyneux/AST Ruby Molyneux.pdf
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send_files failed to open "/tmp/.._AST Ruby Molyneux.pdf.FHvxoI": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Ruby Molyneux/DPS Ruby Molyneux.pdf
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send_files failed to open "/tmp/.._DPS Ruby Molyneux.pdf.xKMtHO": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/ARCHIVED/Ruby Molyneux/Passport Ruby Molyneux.jpeg
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send_files failed to open "/tmp/.._Passport Ruby Molyneux.jpeg.SZJEWK": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/Chloe Ryan/AST Chloe Ryan.pdf
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send_files failed to open "/tmp/.._AST Chloe Ryan.pdf.HU3hUJ": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/Chloe Ryan/Chloe Ryan Passport.pdf
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send_files failed to open "/tmp/.._Chloe Ryan Passport.pdf.kN1xeS": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/Chloe Ryan/DPS Chloe Ryan.pdf
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send_files failed to open "/tmp/..DPS Chloe Ryan.pdf.OWguBr": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/Elena Cami/.DS_Store
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6148 100%    6.99kB/s    0:00:00 (xfer#376, to-check=202/612)
send_files failed to open "/tmp/...DS_Store.8nFSAn": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/Elena Cami/AST Elena Cami.pdf
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send_files failed to open "/tmp/.._AST Elena Cami.pdf.WtI4oa": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/Elena Cami/DPS Elena Cami.pdf
32768  27%   49.23kB/s    0:00:01
117676 100%  176.53kB/s    0:00:00 (xfer#380, to-check=196/612)
send_files failed to open "/tmp/.._DPS Elena Cami.pdf.w0FUuG": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Contracts/Elena Cami/Elena Cami Passport.pdf
32768  38%   40.30kB/s    0:00:01
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send_files failed to open "/tmp/..Elena Cami Passport.pdf.OnI7yM": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/ID/.DS_Store
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6148 100%    7.36kB/s    0:00:00 (xfer#384, to-check=193/612)
send_files failed to open "/tmp/...DS_Store.eAXMkL": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/ID/Lars Fredrik Ridoff - Passport.jpg
32768  13%   30.45kB/s    0:00:06
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send_files failed to open "/tmp/.._Lars Fredrik Ridoff - Passport.jpg.hO1LJ6": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/ID/Tim Crouch passport.jpg
32768   1%  143.50kB/s    0:00:11
1662638 100%    2.01MB/s    0:00:00 (xfer#388, to-check=188/612)
send_files failed to open "/tmp/..Tim Crouch passport.jpg.BCrYGu": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Photos/.DS_Store
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14340 100%   15.07kB/s    0:00:00 (xfer#390, to-check=186/612)
send_files failed to open "/tmp/...DS_Store.MO5yqF": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 1/
send_files failed to open "/tmp/.._Bedroom 1.qDnM3B": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 1.zip
32768  52%   30.92kB/s    0:00:00
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62559 100%   59.03kB/s    0:00:01 (xfer#393, to-check=174/612)
send_files failed to open "/tmp/.._Bedroom 1.zip.sUQJ1a": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 2/
send_files failed to open "/tmp/.._Bedroom 2.HHIiVd": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 2.zip
32768  14%  240.60kB/s    0:00:00
226895 100%    1.61MB/s    0:00:00 (xfer#396, to-check=173/612)
send_files failed to open "/tmp/.._Bedroom 2.zip.DjDJSu": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 3/
send_files failed to open "/tmp/.._Bedroom 3.NH9CYS": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 3.zip
32768   1%  105.26kB/s    0:00:19
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2104623 100%    1.91MB/s    0:00:01 (xfer#399, to-check=172/612)
send_files failed to open "/tmp/.._Bedroom 3.zip.O8QPDZ": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 4/
send_files failed to open "/tmp/.._Bedroom 4.U8d6fa": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 4.zip
32768  31%  246.15kB/s    0:00:00
103208 100%  769.38kB/s    0:00:00 (xfer#402, to-check=171/612)
send_files failed to open "/tmp/.._Bedroom 4.zip.oUfZMd": Operation not permitted
cd+++++++ Dropbox/Stanton House/Howsy/Photos/Flat/
send_files failed to open "/tmp/.._Flat.j9liBx": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Photos/Flat.zip
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send_files failed to open "/tmp/..Flat.zip.93HZcy": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 1/.DS_Store
6148 100%   25.02kB/s    0:00:00
6148 100%   25.02kB/s    0:00:00 (xfer#407, to-check=168/612)
send_files failed to open "/tmp/...DS_Store.ovFzZt": Operation not permitted
f+++++++ Dropbox/Stanton House/Howsy/Photos/Bedroom 1/Bedroom 1 (new pic).jpg
32768   2%   66.53kB/s    0:00:21
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send_files failed to open "/tmp/.._20181130 - Washing Machine installation certificate.pdf.UY0yEZ": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2018-19/20181228 - Microwave replacement.jpg
32768   5%   53.07kB/s    0:00:10
582284 100%  830.13kB/s    0:00:00 (xfer#547, to-check=20/612)
send_files failed to open "/tmp/.._20181228 - Microwave replacement.jpg.8TueTE": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2019-20/20190708_180324.jpg
32768   2%   40.35kB/s    0:00:26
1103673 100%    1.10MB/s    0:00:00 (xfer#549, to-check=16/612)
send_files failed to open "/tmp/.._20190708_180324.jpg.AifTBm": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2019-20/Photo 13-11-2020, 12 50 34.png
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502127 100%  396.09kB/s    0:00:01 (xfer#551, to-check=15/612)
send_files failed to open "/tmp/.._Photo 13-11-2020, 12 50 34.png.FcgixO": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2020-21/Gmail - Your Howsy receipt [#1720-8053].pdf
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send_files failed to open "/tmp/.._Gmail - Your Howsy receipt [#1720-8053].pdf.nhheix": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2020-21/Greenwich Council parking vouchers receipt.pdf
32768  48%    0.00kB/s    0:00:00
67508 100%   33.13MB/s    0:00:00 (xfer#555, to-check=5/612)
send_files failed to open "/tmp/.._Greenwich Council parking vouchers receipt.pdf.jK7aQX": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2020-21/Invoice-76.pdf
32768  37%  231.88kB/s    0:00:00
86783 100%  609.71kB/s    0:00:00 (xfer#557, to-check=4/612)
send_files failed to open "/tmp/.._Invoice-76.pdf.IJrrT7": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2020-21/Invoice-77.pdf
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70285 100%  251.42kB/s    0:00:00 (xfer#559, to-check=3/612)
send_files failed to open "/tmp/.._Invoice-77.pdf.jih8mJ": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2020-21/Photo 01-12-2020, 18 22 44.jpg
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1081344  18%  966.15kB/s    0:00:04
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5825358 100%    1.42MB/s    0:00:03 (xfer#561, to-check=2/612)
send_files failed to open "/tmp/.._Photo 01-12-2020, 18 22 44.jpg.MALizG": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2020-21/Photo 15-10-2020, 18 58 58.jpg
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5408749 100%  427.45kB/s    0:00:12 (xfer#563, to-check=1/612)
send_files failed to open "/tmp/.._Photo 15-10-2020, 18 58 58.jpg.BD4APC": Operation not permitted
f+++++++ Dropbox/Stanton House/Receipts Tax Year 2020-21/Photo 15-10-2020, 20 12 55.jpg
32768   0%   42.05kB/s    0:02:15
1343488  23%    1.22MB/s    0:00:03
5713862 100%    3.14MB/s    0:00:01 (xfer#565, to-check=0/612)
send_files failed to open "/tmp/.._Photo 15-10-2020, 20 12 55.jpg.t1DHWA": Operation not permitted

sent 240886193 bytes  received 12748 bytes  1404658.55 bytes/sec
total size is 240821172  speedup is 1.00
rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.2/rsync/main.c(996) [sender=2.6.9]

I'd try rechecking the source and destination folder (and subfolders eventually when there's a notable difference) sizes with du command – more specifically, du -hd1 <folder path> (or du -d1 <folder path> to see the sizes in raw bytes), Finder may often display differences which are hard to find.
Another recommendation – if you want to back up the whole OS partition, I'd definitely go with Apple's Time Machine – there are many system files, special files, etc. throwing issues when attempted to be handled as regular files where Time Machine does way better job, an example is a /tmp occurrence in your sync dump. You can combine TM with its exclusion list and sync some specific folders another way.
I personally use external drives to store most of the heavy data (photos, movies, music, etc.) so I can easily back up my Macs with Time Machine (Home folder with app preferences, temp downloads etc.) and perform full root backups of external drives with rsync, but back up scenarios really differ from person to person. 😄

Thanks @username0x0a - I did the du commands and it still showed the fairly large differences in the same folders previously identified.

Basically, the idea was to backup my MBAir to my MacMini via wifi, and rather than copy + paste large directories, someone suggested I use rsync so that it just copies what is missing. Sadly it doesn't seem to be working quite as smoothly as hoped!
Time Machine seems best with an external harddrive for backups (not currently with me), so I might just have to resort to copying over the whole directories to my MacMini every couple of weeks or so. I also have iCloud enabled for my most regularly-used files and folders, but was trying to reduce this dependency!
Thanks for all your help though! 5-star support 👍

Will try to run that command later on - but my help may be limited as I'm not a techie! Very good at following instructions and logical checks though :)
I did try a non-Dropbox folder but still encountered differences. Not sure they were as big as this though. Let me try one or two more and get back to you! As it happens, my brother (a techie) said he also encountered some file size differences with video backups but that they also worked fine when opened. He pointed me towards this link but it's a bit too technical for me...! Might make more sense to you though!
Cheers

Will try to run that command later on - but my help may be limited as I'm not a techie! Very good at following instructions and logical checks though :)
I did try a non-Dropbox folder but still encountered differences. Not sure they were as big as this though. Let me try one or two more and get back to you! As it happens, my brother (a techie) said he also encountered some file size differences with video backups but that they also worked fine when opened. He pointed me towards this link but it's a bit too technical for me...! Might make more sense to you though!
Cheers


[HOW-TO] Release camera

After executing following code on raspberry pi 4 i get this error on second capture. It seems like before creating new Picamera, old one needs to be released. How can i do it?
from picamera2 import Picamera2
import time

def capture(image_path):
    camera = Picamera2()
    capture_config = camera.create_still_configuration()
    camera.configure(capture_config)
    camera.start()

    time.sleep(1)
    camera.switch_mode_and_capture_file(capture_config, image_path)

capture('t1.jpg')
capture('t2.jpg')

2022-09-08T11:41:08.214Z | ERROR    | Camera __init__ sequence did not complete.
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/picamera2/picamera2.py", line 123, in __init__
    self._open_camera()
  File "/usr/lib/python3/dist-packages/picamera2/picamera2.py", line 310, in _open_camera
    raise RuntimeError("Failed to acquire camera")
RuntimeError: Failed to acquire camera

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/pi/pythoncamera/test.py", line 14, in <module>
    capture('t2.jpg')
  File "/home/pi/pythoncamera/test.py", line 5, in capture
    camera = Picamera2()
  File "/usr/lib/python3/dist-packages/picamera2/picamera2.py", line 130, in __init__
    raise RuntimeError("Camera __init__ sequence did not complete.")
RuntimeError: Camera __init__ sequence did not complete.

The following did the trick for me -
camera.close()

thanks


EmptyPoint = Point(-1, -1) is incorrect

Description
The following is a bug: https://github.com/Shopify/react-native-skia/blob/main/package/cpp/rnskia/dom/props/PointProp.h#L20 (it marks a {-1, -1} point as invalid)
As showcased in the following failing test: https://github.com/Shopify/react-native-skia/pull/1222/files#diff-6a8885be7798af3857619c064fab56d917fd146cdac19aa3d6686923e843017bR7
Should this be aligned with other property and return nullptr if invalid? Or throw an error?
Version
latest
Steps to reproduce
run the following test: https://github.com/Shopify/react-native-skia/pull/1222/files#diff-6a8885be7798af3857619c064fab56d917fd146cdac19aa3d6686923e843017bR7
Snack, code example, screenshot, or link to a repository
https://github.com/Shopify/react-native-skia/pull/1222/files#diff-6a8885be7798af3857619c064fab56d917fd146cdac19aa3d6686923e843017bR7

Good point! I think we should align and NOT use {-1, -1} as the none value.


Smoother liftover for working with ranges in different genome builds

Improve liftover operation for working with GRanges. This probably should live in a new package, maybe easylift? I'd be happy to work with someone interested in writing their first Bioconductor package.
Currently the operations are:

Find chain file on UCSC website
Download
Unzip
rtracklayer::import
rtracklayer::liftOver
unlist
genome()<- (what about seqinfo/seqlengths?)

From Herve (on tech-advisory-board channel)
"With this improvement to getChromInfoFromUCSC(), the standard way to set the Seqinfo on the lifted object becomes:"
to_seqinfo <- getChromInfoFromUCSC("hg19", assembled.molecules.only=TRUE, as.Seqinfo=TRUE)
lifted_seqlevels <- seqlevels(cur)[genome(cur) %in% "hg38"]
seqinfo(cur19) <- update(seqinfo(cur19), to_seqinfo[lifted_seqlevels])

with the relevant commit to GenomeInfoDb:
https://github.com/Bioconductor/GenomeInfoDb/commit/345f22c55b8c431f1cf8080af3235f78266ade9c

I created this Issue to link the repo to the Tidyomics Open Challenges project.
I archived the original issue

FYI in github you can transfer issues from one repo to another.

This is great, and already looks very useful.
I have a few notes/suggestions:

if the incoming object has no seqinfo (besides genome), then the outgoing object only has seqinfo on the seqnames that are represented by ranges in gr. I think it would be preferable to output the comprehensive seqinfo (to_genome_info) in this case
maybe you can test if the chain is gzipped, and if so unzip it for the user, see file_ext and unzip
going further, it would be cool to have the ability for user not to specify chain if there exists a file already in BiocFileCache, see below for example:

# the user should do these steps manually, e.g. downloading the chain file, and adding to BFC:
library(BiocFileCache)
bfc <- BiocFileCache()
bfcadd(bfc, "hg19ToHg38.over.chain", "/path/to/hg19ToHg38.over.chain")
# now your function could use the following steps to retrieve a previously cached resource:
q <- bfcquery(bfc, "hg19ToHg38.over.chain")
nrow(q)
q$rid
bfc[[q$rid]]
import(bfc[[q$rid]])

Thank you for the suggestions. I have pushed code for .gz file support.
if the incoming object has no seqinfo (besides genome)
Can you kindly provide the gr for such an object in the context of the code below? Thanks
gr <- GRanges(seqname = Rle(paste("chr", 1, sep = "")),
              ranges = IRanges(start = 1, end = 200000))
genome(gr) <- "hg19"
to <- "hg38"
chain <- "data/hg19ToHg38.over.chain.gz"
lifted <- easylift(gr, to, chain)

will review and provide an example soon

Your current example gives:
!> seqinfo(lifted)
 Seqinfo object with 2 sequences from hg38 genome:
   seqnames seqlengths isCircular genome
   chr1      248956422      FALSE   hg38
   chr19      58617616      FALSE   hg38

I think it should just return the complete seqinfo.
I'll push a suggested change in one minute.

I think this is right actually 34777ce
...its different than the original suggestion, but I think the original suggestion wasn't correct. It doesn't make sense to only update the sequences with ranges represented in gr, because you end up with a mix of different builds. We should just replace the entire set of sequences with to_seqinfo.

Idea: you could maybe now start moving this function into a Bioconductor package using biocthis.
I can give some assistance afterward with the BiocFileCache idea.

@mikelove awesome! thank you so much for the push. I will turn this into a package using biocthis

@mikelove package development initiated and it builds properly. Can be installed and used as well. Just tried the code below and it works:
BiocManager::install("nahid18/easylift")
BiocManager::install("GenomicRanges")

library("easylift")
library("GenomicRanges")

gr <- GenomicRanges::GRanges(seqname = Rle(paste("chr", 1, sep = "")),
              ranges = IRanges(start = 1, end = 200000))
genome(gr) <- "hg19"
to <- "hg38"
chain <- "hg19ToHg38.over.chain.gz"

lifted <- easylift(gr, to, chain)

seqinfo(gr)
seqinfo(lifted)

Great! I’ll take a look soon

I just took a shot at adding BiocFileCache support, wanna try it?

Kind of magical
> gr |> easylift("hg38")
GRanges object with 2 ranges and 0 metadata columns:
      seqnames        ranges strand
         <Rle>     <IRanges>  <Rle>
  [1]     chr1  10001-177376      *
  [2]    chr19<PHONE_NUMBER>64      *
  -------
  seqinfo: 25 sequences (1 circular) from hg38 genome

Kind of magical
> gr |> easylift("hg38") # chr5:1e6-2e6, hg19
GRanges object with 2 ranges and 0 metadata columns:
      seqnames          ranges strand
         <Rle>       <IRanges>  <Rle>
  [1]     chr5<PHONE_NUMBER>328      *
  [2]     chr5 1785330-1999886      *
  -------
  seqinfo: 25 sequences (1 circular) from hg38 genome

wow! this is indead magical! thank you so much! @mikelove

@nahid18  please add your authorship details here https://docs.google.com/spreadsheets/d/19XqhN3xAMekCJ-esAolzoWT6fttruSEermjIsrOFcoo/edit?usp=sharing

@mikelove Submitted the package to Bioconductor: https://github.com/Bioconductor/Contributions/issues/3122

Nice! 🎉
Open issue to first R package in a few weeks.


the script does not install anything

The script hangs on the installation, I left it for 3 hours and in the end it showed that the services needed for the installation were loaded, but I did not find them anywhere on my computer. It also happened with the samsung applications themselves. I will be very grateful for any help.

Could you check if they're available on the windows store?


Customizable Intellisense

I would like to be able to have a file (like a .json file), in which you are able to custimize Intellisense.
For Example, I have made a custom python module and it would be cool, if for example the method
text_at(line, "text", "alignment") would then trigger intellisense to suggest the numbers 1 to 13 as parameter line and so on.
I imagine, that you could make it like this (similar to snippets):
{
   "Custom Intellisense Part Name": {
   "scope": "python",
   "method": "class.function",
   "argument_number": "0",
   "autocomplete_type": "[like_these](https://code.visualstudio.com/docs/editor/intellisense#_types-of-completions)",
   "suggestions": [
       1, 2, 3, 4, 5, 6, 7, 8, 9, 10, "11"
       ]
    }

}

maybe also add a description argument to the intellisense for better understanding


ms_label only 0 and 10, not have 1 - 9

But I have met other problems, ms_label only 0 and 10, not have 1 - 9 kinds.
Currently testing images in mountainous areas. (use Sentinel-2 RGB bands image)
What should I consider when test images?
Originally posted by @daniellinboy in https://github.com/jensleitloff/CNN-Sentinel/issues/8#issuecomment-547487455

@daniellinboy What data are you using? Does the test data have the same classes as the training data? Are you sure, that the order of the Sentinel-2 bands is correct?

As you are using RGB images, check correct scaling. We already addressed this in issue #1.

Thank you again for your valuable suggestions.
@felixriese
I trained the data using EuroSAT data and then tested the area almost in the mountains.
Thank you for your reminder, I forgot to sure the test area with similar training data. attachment_test area
@jensleitloff
I am not using the code, I also guess that there will be a scale problem, thank you for providing such a good solve direction.

@daniellinboy I am not sure how to use your example image. Is the issue resolved?


Report failure when provider fails to configure network

When the provider fails to configure the network, it reports an appropriate exception. The exception is handled so that the migration cases like rollback is supported, but the exception needs to be raised for non migration cases.

Is this the BZ for 17?
https://bugzilla.redhat.com/show_bug.cgi?id=2313764
What is the Jira for this patch?


Improves handling when Tar is pointed directly at a file.

This addresses a bug (#ENGT-1779) where an invalid tarball was created when
tarhelper.NewTar is pointed directly at a file rather than a directory.
Previously, it would create a tarball with the file just fine, but the file in
the tarball would be named ".".
When then untaring the file, it would simply not work too well. If the
NewUntar path already existed, it would error, or if it didn't exist, create
the target but the caller is often expecting a path, while it would create it
as a file.
This change improves the handling, where when it is pointed at a file, it will
tar just the file, but preserve its filename as the entry, and when the same
file is untarred, the target would be a path and it would contain the
specified file.
@alextoombs @klobucar

LGTM


Generate ACME Certificate

Is it possible to generate a acme certificate (acme.json) rather than .pem and .key file?

Purely theoretically, it is possible to make an alternative output in acme.json. If it looks something like this (indicated below), then in principle all the data is there and such a file can be generated.
{
  "Account": {
    "Email"<EMAIL_ADDRESS>    "Registration": {
      "body": {
        "status": "valid",
        "contact": [
<EMAIL_ADDRESS>        ]
      },
      "uri": "https://acme-v02.api.letsencrypt.org/acme/acct/XXXX"
    },
    "PrivateKey": "xxxx",
    "KeyType": "2048"
  },
  "Certificates": [
    {
      "Domain": {
        "Main": "domain.com",
        "SANs": ["san.domain.com"]
      },
      "Certificate": "xxx",
      "Key": "xxx"
    }
  ],
  "HTTPChallenges": null,
  "TLSChallenges": {}
}

Got it, previously I wanted to use the free domain(.tk) to get a subdomain SSL wild card using Traefik.
Traefik connects to the service provider (ex: Cloudflare) and generates the ACME Certificate.
But since Cloudflare doesn't support free domain DNS records, I can't get the certificate.
I thought I could generate an ACME Certificate on my own and get the job done.
Nevertheless, I gave up to use the free domain and buy a domain to settle my issue.
Thank you AMEST for helping me!