From unknown Fri Aug 15 15:34:45 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#65101 <65101@debbugs.gnu.org> To: bug#65101 <65101@debbugs.gnu.org> Subject: Status: Singularity can't find basic programs Reply-To: bug#65101 <65101@debbugs.gnu.org> Date: Fri, 15 Aug 2025 22:34:45 +0000 retitle 65101 Singularity can't find basic programs reassign 65101 guix submitter 65101 "N. 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Y." Date: Sat, 5 Aug 2023 16:22:07 +0000 Message-ID: Subject: Singularity can't find basic programs To: bug-guix@gnu.org Content-Type: multipart/alternative; boundary="000000000000412f3e06022f6c53" Received-SPF: pass client-ip=2607:f8b0:4864:20::734; envelope-from=ningyuan.sg@gmail.com; helo=mail-qk1-x734.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, WEIRD_PORT=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) --000000000000412f3e06022f6c53 Content-Type: text/plain; charset="UTF-8" On guix (GNU Guix) 5aceacac65784bd2e1fd12304f965ae6026de49d, trying to build a Singularity image, I get many "command not found" errors for the programs id, install, zcat, and tar: ning@bluecoral ~/repos/bento$ sudo singularity build bento.sif bento.def Password: Using container recipe deffile: bento.def Sanitizing environment /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/functions: line 34: id: command not found /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/functions: line 34: id: command not found /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-scripts/pre.sh: line 44: install: command not found /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-scripts/pre.sh: line 45: install: command not found /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-scripts/pre.sh: line 46: install: command not found egrep: warning: egrep is obsolescent; using grep -E /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/functions: line 34: id: command not found Adding base Singularity environment to container /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-scripts/environment.sh: line 45: zcat: command not found /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-scripts/environment.sh: line 45: tar: command not found Cleaning up... In my system.scm, I have both the singularity package: ;; Packages installed system-wide. Users can also install packages ;; under their own account: use 'guix search KEYWORD' to search ;; for packages and 'guix install PACKAGE' to install a package. (packages (append (map specification->package '("nss-certs" "ntfs-3g" "singularity")) %base-packages)) As well as the service: ;; Below is the list of system services. To search for available ;; services, run 'guix system search KEYWORD' in a terminal. (services (append (list (service gnome-desktop-service-type) (service cups-service-type ; http://localhost:631 (cups-configuration (web-interface? #t))) (service bluetooth-service-type) (set-xorg-configuration (xorg-configuration (keyboard-layout keyboard-layout))) (service docker-service-type) (service singularity-service-type)) ;; This is the default list of services we ;; are appending to. %desktop-services)) p.s. I also cannot build images without sudo, but I do not know if this is intended: ning@bluecoral ~/repos/bento$ singularity build bento.sif bento.def Using container recipe deffile: bento.def ERROR: You must be the root user to build from a Singularity recipe file Cleaning up... Best regards, Ning --000000000000412f3e06022f6c53 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
On=C2=A0guix (GNU Guix) 5aceacac65784bd2e1fd12304f965ae602= 6de49d, trying to build a Singularity image, I get many "command not f= ound" errors for the programs id, install, zcat, and tar:

=
ning@bluecoral ~/repos/bento$ sudo singularity build bento.sif b= ento.def
Password:
Using container recipe deffile: bento.def
San= itizing environment
/gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singular= ity-2.6.1/libexec/singularity/functions: line 34: id: command not found
= /gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singu= larity/functions: line 34: id: command not found
/gnu/store/cg4mz2irhcjc= md6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-script= s/pre.sh: line 44: install: command not found
/gnu/store/cg4mz2irhcjcmd6= ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-scripts/p= re.sh: line 45: install: command not found
/gnu/store/cg4mz2irhcjcmd6ngs= zc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-scripts/pre.= sh: line 46: install: command not found
egrep: warning: egrep is obsoles= cent; using grep -E
/gnu/store/cg4mz2irhcjcmd6ngszc04prn6xqvlqj-singular= ity-2.6.1/libexec/singularity/functions: line 34: id: command not found
= Adding base Singularity environment to container
/gnu/store/cg4mz2irhcjc= md6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-script= s/environment.sh: line 45: zcat: command not found
/gnu/store/cg4mz2irhc= jcmd6ngszc04prn6xqvlqj-singularity-2.6.1/libexec/singularity/bootstrap-scri= pts/environment.sh: line 45: tar: command not found
Cleaning up...

In my system.scm, I have both the singularity packa= ge:

=C2=A0 ;; Packages installed system-wide.=C2= =A0 Users can also install packages
=C2=A0 ;; under their own account: u= se 'guix search KEYWORD' to search
=C2=A0 ;; for packages and &#= 39;guix install PACKAGE' to install a package.
=C2=A0 (pa= ckages (append (map specification->package '("nss-certs" &= quot;ntfs-3g" "singularity"))
=C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 %base-packages))
<= br>
As well as the service:

=C2=A0 ;; Be= low is the list of system services.=C2=A0 To search for available
=C2=A0= ;; services, run 'guix system search KEYWORD' in a terminal.
= =C2=A0 (services
=C2=A0 =C2=A0(append (list (service gnome-desktop-servi= ce-type)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(= service cups-service-type
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0; http://localhost= :631
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0(cups-configuration (web-interface? #t)))
=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(service bluetooth-service-type)
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(set-xorg-con= figuration
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 (xorg-configuration (keyboard-layout keyboard-layout)))
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(service docker-service= -type)
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(se= rvice singularity-service-type))
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0;; This is the default list of services we
=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0;; are appending to.
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0%desktop-services))

p.s. I also cannot = build images without sudo, but I do not know if this is intended:

ning@bluecoral ~/repos/bento$ singularity build bento.sif b= ento.def
Using container recipe deffile: bento.def
ERROR: You must b= e the root user to build from a Singularity recipe file
Cleaning up...

Best regards,
Ning
--000000000000412f3e06022f6c53--